I have some ATACseq bam files and a reference peak set(genomic regions) in text format. I am trying to get count matrix from the bam files( i.e or each bam file I want to calculate f how many reads fall in each peak) . so I am trying to use
featureCounts for this purpose. which needs annotations in SAF or GTF format. 1) in my case is annotation the reference peakset ? 2) if so how to convert my peak set to
GTF format .
here is a few lines of the peak set
seqnames start end name score annotation percentGC chr1 906012 906513 ACC_10 7.171192997 Intron 0.612774451 chr2 112541661 112542162 ACC_10008 22.03057903 Promoter 0.55489022 chr1 21673421 21673922 ACC_1001 6.459954383 Distal 0.508982036 chr2 112584205 112584706 ACC_10013 43.20855549 Promoter 0.586826347 chr2 112596243 112596744 ACC_10016 5.428209077 Intron 0.491017964 chr1 21725692 21726193 ACC_1002 5.201272875 Intron 0.405189621