boncey
ATACseq RGT HINT Footprinting- 0 Footprints
ATACseq RGT HINT Footprinting- 0 footprints
I am attempting to analyze ATACseq data using RGT HINT. I have sorted and indexed .bam files that are ready to be foot printed, and there is no error message when I run the code, but it outputs an empty footprint file and gives me the following info file. Number of reads: 49618692 Number of peaks: 92291 Number of tag counts within peaks: 17685263.0 Number of footprints: 0 So it is able to detect the reads, but detects zero footprints. Using IGV, I can see that my .bam files look correct and contains chromosomal information. Has anyone else had this issue? What could be the problem here?
My one theory is that it is a problem with matching to the reference genome (hg38). When I generate headers for my bam file, it seems to only contain the non-chromosomal regions. There are no chromosomal names in the headers. However, once again the file looks right on IGV. But it seems to not be able to match the reads to the reference genome.
