Hi,

I am running the Peakranger ccat algorithm (to find broad peaks):

PeakRanger-1.17/bin/peakranger ccat --format bam -d IP.bam -c input.bam  --report -q 0.01  --output results --gene_annot_file mm10_ref

I am using the reference for mm10 from the Peakranger site: http://ranger.sourceforge.net/manual1.18.html

BUT all the results I get are marked as strand + and I know for sure that there are - in there, as I checked the locations using the summit files.

So I guess I am missing something, as it does not read the strand from the GTF correctly.

I couldn't find any reference to this in the documentation. Anyone know where the issue might lie?

Thanks,