I've got some non-stranded libraries that I have aligned with STAR-RSEM. I now want to use StringTie to discover new transcripts. My problem is that StringTie seems to accept --rf or --fr for library orientation (StringTie/1.3.3) but there's no option for non-stranded libraries. So apparently if using STAR alone I could do "--outSAMstrandField intronMotif", which would add and XS tag, which in turn, it will be read by StringTie. Unfortunately that option is not available when using "rsem-calculate-expression". Is there any way I can solve my issue using RSEM?
Thank you very much for your time and help,
Hi,
I've got some non-stranded libraries that I have aligned with STAR-RSEM. I now want to use StringTie to discover new transcripts. My problem is that StringTie seems to accept --rf or --fr for library orientation (StringTie/1.3.3) but there's no option for non-stranded libraries. So apparently if using STAR alone I could do "--outSAMstrandField intronMotif", which would add and XS tag, which in turn, it will be read by StringTie. Unfortunately that option is not available when using "rsem-calculate-expression". Is there any way I can solve my issue using RSEM? Thank you very much for your time and help,
ml439