ChIPSeqFPro, a pipeline for sequential processing of ChIP-Seq fastq to bigwig files

Pjanic, M.

doi:10.1101/118281

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bioRxiv · 10.1101/118281

ChIPSeqFPro, a pipeline for sequential processing of ChIP-Seq fastq to bigwig files

Pjanic, M.

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Abstract

ChIPSeqFPro is a pipeline that automates processing of a collection of ChIPSeq or ATAC-Seq data starting from the gzip compressed fastq files. It performs the quality control using FastQC, mapping to the human genome hg19 or mouse mm10 using BWA mapper, for both single read or paired end sequencing fastq files, followed with sam to bam conversion using samtools view, creates statistics on bam files using samtools flagstat, peak calling with MACS, and finally creates high resolution bigwig files from bam files using a custom script bam2bigwig that invokes bedtools bamtobed and UCSC scripts, bedItemOverlapCount, bedGraphToBigWig and fetchChromSizes.

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Pjanic, M.. 2017-03-18. ChIPSeqFPro, a pipeline for sequential processing of ChIP-Seq fastq to bigwig files. https://doi.org/10.1101/118281

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