Extracting the sequence of isoforms from RNA-seq data

Question

[pixie@bioinfo]

Hello, I have a basic doubt. I have used rMATs to predict alternative splice events in my data. Then I am using IGV to built the sashimi plots to view the junction and exonic reads. Any idea how to extract the sequence for the isoforms ? The organism I am working on has the sequences given only for the primary transcript. How do I extract the novel isoform sequences ?

Thanks.

Answer 1

[michael.ante]

Hi Pixie,

There are some tools available:

• StringTie's / Cufflink's gffread
• Bedtools getFastaFromBed
• BedOps bed2faidx

Cheers,

Michael

[pixie@bioinfo]

Thanks Michael, I will check those out!