Reconstruct mRNA isoform sequences from RNAseq data (+ genome edition)

Question

[Aurelie MLB]

Hello,

Is it possible to reconstruct the sequences of the mRNA isoforms present in a sample from RNA seq data please? Which tool would you use (if there are some) or how would you do?

If there are some tools would you know how they would cope with genome edition (~50 nt deletion) being done prior to the RNA seq experiment ? (as the edition will potentially lead to new/unknown mRNA being generated)

Any advice or comment would be helpful. Thanks in advance!

[Devon Ryan]

I assume the answer is "yes", but am I correct in assuming that you have a reference genome?

[Aurelie MLB]

I do have a reference genome yes. Thanks !

Answer 1

[h.mon]

check Recommended Tools For Alternative Splicing Detection From Rna-Seq Data question.

Answer 2

[Devon Ryan]

Check out the "transcriptome assemblers" in the post linked to by Recommended Tools For Alternative Splicing Detection From Rna-Seq Data and I'll add stringTie to that, which is probably the one I'd first try.

[Aurelie MLB]

Thanks a lot to h.mon and Ryan for pointing me to this post!