Dear reader,

I have a stranded total RNA-seq library from which I am interested in identifying antisense transcripts and cryptic transcripts. Although I have already already attempted to find the antisense transcripts by the strategy outlined below, I wanted to know the caveats of this approach and if there are any additional ways to identify such transcripts. If you have done this kind of analysis before or could refer me to some online material, I will be really grateful.

Strategy used: Sorted BAM files -> StringTie Assembly -> gffcompare -> extract class x/u transcripts -> BEDtools antisense overlaps -> DESeq2 on transcripts found -> IGV validation

Thanks a lot for your time in advance!