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07. STAR: map transcript reads to the reference genome and identify splice junctions
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07. STAR: map transcript reads to the reference genome and identify splice junctions
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#!/bin/bash
#SBATCH -n 16
#SBATCH --mem-per-cpu=16000
#SBATCH --job-name=STAR_sexSpecificGenome_VP46.sh
#SBATCH -t 2-0:0
#SBATCH -A mwilsons
#SBATCH -o slurm.STAR_sexSpecificGenome_VP46.sh.out
#SBATCH -e slurm.STAR_sexSpecificGenome_VP46.sh.err
#SBATCH --mail-type=END,FAIL
#SBATCH [email protected]
#--------------------------
#--------------------------
# 1. start timer
#--------------------------
date
#--------------------------
# 2. move to directory and load programs
#--------------------------
cd /scratch/kcolney/cancerCellLines_Haynes
module load star/2.4.2a
#--------------------------
# 3. STAR read aligner pass 1
#--------------------------
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH1_S1_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH1_S1_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH1_S1_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH1_S1_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH1_S1_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH1_S1_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH1_S1_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH1_S1_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH2_S2_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH2_S2_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH2_S2_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH2_S2_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH2_S2_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH2_S2_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH2_S2_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH2_S2_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH3_S3_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH3_S3_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH3_S3_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH3_S3_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH3_S3_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH3_S3_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH3_S3_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH3_S3_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH4_S4_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH4_S4_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH4_S4_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH4_S4_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH4_S4_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH4_S4_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH4_S4_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH4_S4_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH5_S5_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH5_S5_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH5_S5_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH5_S5_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH5_S5_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH5_S5_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH5_S5_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH5_S5_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH6_S6_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH6_S6_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH6_S6_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH6_S6_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH6_S6_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH6_S6_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH6_S6_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH6_S6_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH7_S7_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH7_S7_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH7_S7_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH7_S7_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH7_S7_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH7_S7_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH7_S7_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH7_S7_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH8_S8_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH8_S8_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH8_S8_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH8_S8_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH8_S8_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH8_S8_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH8_S8_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH8_S8_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH9_S1_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH9_S1_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH9_S1_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH9_S1_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH9_S1_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH9_S1_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH9_S1_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH9_S1_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH10_S2_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH10_S2_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH10_S2_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH10_S2_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH10_S2_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH10_S2_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH10_S2_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH10_S2_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH11_S3_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH11_S3_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH11_S3_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH11_S3_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH11_S3_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH11_S3_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH11_S3_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH11_S3_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH12_S4_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH12_S4_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH12_S4_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH12_S4_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH12_S4_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH12_S4_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH12_S4_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH12_S4_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH13_S5_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH13_S5_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH13_S5_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH13_S5_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH13_S5_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH13_S5_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH13_S5_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH13_S5_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH14_S6_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH14_S6_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH14_S6_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH14_S6_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH14_S6_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH14_S6_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH14_S6_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH14_S6_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH15_S7_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH15_S7_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH15_S7_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH15_S7_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH15_S7_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH15_S7_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH15_S7_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH15_S7_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH16_S8_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH16_S8_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH16_S8_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH16_S8_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH16_S8_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH16_S8_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH16_S8_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH16_S8_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH17_S9_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH17_S9_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH17_S9_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH17_S9_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH17_S9_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH17_S9_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH17_S9_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH17_S9_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH18_S9_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH18_S9_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH18_S9_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH18_S9_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH18_S9_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH18_S9_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH18_S9_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH18_S9_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH19_S10_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH19_S10_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH19_S10_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH19_S10_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH19_S10_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH19_S10_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH19_S10_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH19_S10_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH20_S10_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH20_S10_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH20_S10_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH20_S10_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH20_S10_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH20_S10_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH20_S10_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH20_S10_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH21_S11_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH21_S11_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH21_S11_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH21_S11_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH21_S11_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH21_S11_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH21_S11_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH21_S11_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH22_S11_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH22_S11_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH22_S11_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH22_S11_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH22_S11_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH22_S11_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH22_S11_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH22_S11_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH23_S12_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH23_S12_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH23_S12_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH23_S12_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH23_S12_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH23_S12_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH23_S12_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH23_S12_L004_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH24_S12_L001_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH24_S12_L001_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH24_S12_L002_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH24_S12_L002_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH24_S12_L003_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH24_S12_L003_pass1. --runThreadN 8
STAR --genomeDir /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64 --sjdbGTFfile /scratch/kcolney/cancerCellLines_Haynes/GRCh38_Y_excluded_VP64/gencode.v25.chr_patch_hapl_scaff.annotation.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --readFilesIn /home/kcolney/cancer_HaynesLab/trim_eachlane/KH24_S12_L004_Trim_430minlen50.fastq --outSAMtype BAM Unsorted --outFileNamePrefix /scratch/kcolney/cancerCellLines_Haynes/STAR_pass1/KH24_S12_L004_pass1. --runThreadN 8
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# 4. end timer
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