6.6 years ago by
"Transitionally active" is not something you can determine computationally. Someone needs to have done an experiment on your tissue to determine if that bit of sequence is transcribed in your tissue.
Bowtie or bwa will tell you if your read runs forward or reverse with regard to your reference sequence, but what reference sequence are you using? If your reads are from spliced transcripts, you either need to be aligning to a file of spiced transcripts, or to the genome using an aligner that is "splice-aware" and will try to align reads with giant gaps where introns are. Bowtie's sister program TopHat will do this, bwa will not. If you align to genome, and find that your read is in a transcript, you will need to determine whether that gene runs forward or backwards with respect to the genome.