I have paired end stranded rnaseq data (trueseq stranded dutp protocol), Intially i incorrectly used - - fr option instead of rf. However, even with correct rf option for this protocol, i noticed that expression of a gene i was looking at is zero (rna direction is 3' to 5'), though are enough reads to support mapping when i visualise it through igv and it gives certain tpm value with unstranded option as well. If there are many cases like this, then i may loose important candidates. Please guide, may be i am missing some important point.
P. S. I posted this on kallisto-sleuth user group as well but didn't have reply yet.
Thanks in advance!!