scripts for processing NGS data including: ChIP-seq, RNA-seq, ATAC-seq

There are the pipeline scripts I wrote for processing ChIP-seq, RNA-seq and ATAC-seq data.

Name		Name	Last commit message	Last commit date
Latest commit History 17 Commits
example		example
ATAC_functions.R		ATAC_functions.R
DESeq2_functions.R		DESeq2_functions.R
NexteraPE-PE.fa		NexteraPE-PE.fa
README.md		README.md
STAR_index.sh		STAR_index.sh
adjustBedTn5.sh		adjustBedTn5.sh
commit.sh		commit.sh
create_hg19.exon.genes.R		create_hg19.exon.genes.R
fastq2bam_PE_bowtie.sh		fastq2bam_PE_bowtie.sh
fastq2bam_PE_star.sh		fastq2bam_PE_star.sh
fastq2bam_SE_bowtie.sh		fastq2bam_SE_bowtie.sh
fastq2bam_SE_star.sh		fastq2bam_SE_star.sh
filter.R		filter.R
fraglen_distribution.R		fraglen_distribution.R
get_seqs.R		get_seqs.R
helper.R		helper.R
makeBW.R		makeBW.R
makeBW2.R		makeBW2.R
makeBW_atac.R		makeBW_atac.R
make_bed_atac.R		make_bed_atac.R
step1.sh		step1.sh
step2_SE.sh		step2_SE.sh
step2_SE_RNAseq.sh		step2_SE_RNAseq.sh

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