Antisense transcription quantification

[ngualand]

Hi,

I'm interested in the quantification of antisense transcripts derived from TEs, I wonder whether I can use for quantification the reported TEs that have a tx_strand opposite to the te_strand? Or I should re-run the analysis using the opposite strand orientation(e.g if I normally use 2 can I use 1?)

What will be the best approach by using your software?

Thanks