transcript_assembly.sh

#!/bin/bash
#SBATCH --job-name=sam_sort_bam
#SBATCH --mail-user=
#SBATCH --mail-type=ALL
#SBATCH -n 1
#SBATCH -N 1
#SBATCH -c 16
#SBATCH --mem=120G
#SBATCH -o sam_sort_bam_%j.out
#SBATCH -e sam_sort_bam_%j.err
#SBATCH --partition=general

export TMPDIR=/home/CAM/$USER/tmp/

module load gffread
module load stringtie

gffread TAIR10_GFF3_genes.gff -T -o athaliana_TAIR10_genes.gtf

stringtie -p 16 athaliana_root_1.bam -G athaliana_TAIR10_genes.gtf -o athaliana_root_1.gtf

stringtie -p 16 athaliana_root_2.bam -G athaliana_TAIR10_genes.gtf -o athaliana_root_2.gtf

stringtie -p 16 athaliana_shoot_1.bam -G athaliana_TAIR10_genes.gtf -o athaliana_shoot_1.gtf

stringtie -p 16 athaliana_shoot_2.bam -G athaliana_TAIR10_genes.gtf -o athaliana_shoot_2.gtf

stringtie --merge -p 16 -G -o merged stringtie_merged.gtf

stringtie -e -B -p 16 athaliana_root_1.bam -G stringtie_merged.gtf -o ballgown/athaliana_root_1/athaliana_root_1.count

stringtie -e -B -p 16 athaliana_root_2.bam -G stringtie_merged.gtf -o ballgown/athaliana_root_2/athaliana_root_2.count

stringtie -e -B -p 16 athaliana_shoot_1.bam -G stringtie_merged.gtf -o ballgown/athaliana_shoot_1/athaliana_shoot_1.count

stringtie -e -B -p 16 athaliana_shoot_2.bam -G stringtie_merged.gtf -o ballgown/athaliana_shoot_2/athaliana_shoot_2.count