Finding Novel Transcripts From A De Novo Transcriptome Assembly

Question

[ilovepython]

I've assembled a de novo transcriptome from RNAseq data. I'm comparing it against a reference cDNA set that is publicly available. However, I'd like to see if my assembly has produced any novel transcripts. Is there something like a reverse alignment? I'd like to find transcripts that I've assembled that are not included in this file of cDNA. I will then map them to the genome using blat or a similar tool.

How can I do what seems like the inverse of an alignment?

Answer 1

[Nicolas Rosewick]

Check here :

Extract Unmapped Reads From Blast