ChIPseqPipeline is a NGS ChIP-seq data processing pipeline. It aligns the sequenced reads in the fastq format to the genomic sequence and produces the files suitable for downstream analysis and viewing of aligned reads on the genome browsers. The pipeline uses Bowtie2 program for aligning the reads to the indexed genome builds. It can handle both the single end reads, and the paired-end reads. The output contains bed/bam files for further analysis, and bigwig files which could be loaded on a genome browser. The pipeline uses samtools for the conversion of data formats. https://github.com/narekum/ChIPseqPipeline
ChIPseq-Pipeline
