ATAC-Seq-pipeline

A pipeline of ATAC-Seq raw data processing and downstream analysis

Options:

-h --help      display the usage and exit.
-a --access    necessary file containing SRR number or sample name to be operate. [e.g. accession.txt]
-d --dump      transform sra to fastq by fastq-dump.
-f --fastp     perform QC to sample by fastp with the default parameters,the sequencing type P/S must be provided.(Pair end and Single end) [e.g. P/S]
-c --cut       specify two comma separated INT parameters to cutadapte for sample. [e.g. 15,0]
-b --bowtie2   use bowtie2 to map the clean data to the REFERENCE and transform to the bam file
-s --sort      use samtools to sort the bam file
-p --picard    use picard to remove duplicates
-r --remove    remove unwanted reads using samtools
-D --deeptools use deeptools to get BigWiggle from sorted bam for drawing gene profile
-P --peaks     use macs2 to call peaks from filtered bam
-H --HOMER     use HOMER to find Motifs and TFBS
-g --graph     transform to bigWig Format for genome browser
-v --version   display version information and exit.\n"

Example

sh ATAC_pipeline.sh -a accession.txt -d -f S -c 5,3 -b -s -p -r -D -P -H -g