I am working with Tophat2 and HTSeq-count until now but, I want to use HISAT2 and learn about it. For that, I have been trying and working with this tool this week. Everything was fine until I tried to calculate the count from the SAM files using HTSeq-count. When I used this tool for the count, all the transcript counts in the output files are 0. This represents a real problem for me because I need to use HTSeq-count to keep the same distribution than the data that I already have.
So, Is it possible to use these two tools together? or Is there another tool that mantain the same distribution in the output file that HTSeq-count but works with HISAT2?
Both HISAT2 and HTSeq-count are in their last version.
Thank you in advance for your time.