Hi, I'm new to this area so forgive me for asking a probably very simple question.
I'm just starting a project involved with looking for evidence of antisense expression. I have got single end, strand-specific RNA-seq data, using the dUTP method.
I want to use HTseq-count to count the reads. I was informed that if I use the --stranded=yes option, this will give me all the anti-sense expression counts. And if I use the --stranded=reverse option, this will give me all the sense counts.
However on doing further reading, I'm beginning to think that this may not be the case. As i read that when --stranded=yes, HTSEQ-count only counts reads only if the strand information in both the SAM file and GFF file is the same. With the opposite being true for --stranded=reverse.
I was wondering if someone could suggest which option I should be using and why.
Thanks, I really do appreciate anything you can provide.
I'm just starting a project involved with looking for evidence of antisense expression. I have got single end, strand-specific RNA-seq data, using the dUTP method.
I want to use HTseq-count to count the reads. I was informed that if I use the --stranded=yes option, this will give me all the anti-sense expression counts. And if I use the --stranded=reverse option, this will give me all the sense counts.
However on doing further reading, I'm beginning to think that this may not be the case. As i read that when --stranded=yes, HTSEQ-count only counts reads only if the strand information in both the SAM file and GFF file is the same. With the opposite being true for --stranded=reverse.
I was wondering if someone could suggest which option I should be using and why.
Thanks, I really do appreciate anything you can provide.