version1.0

Version 1

• Initial quality check with FastQC and MultiQC.
• Alignment with Bowtie2. Alignment parameters are based on the recommendation by Henikoff et.al.
• File conversion, sorting, and indexing with samtools.
• Removal of low quality reads (MAPQ<30).
• Removal of reads mapped to blacklist region.
• MACS2 peak calling.
• 500k bin count matrix formation.
• Reads normalization with TMM (normalization method from edgeR).
• Coverage files generation (bigwig files)