Question: Extracting the sequence of isoforms from RNA-seq data
0
gravatar for pixie@bioinfo
8 months ago by
pixie@bioinfo1.4k
pixie@bioinfo1.4k wrote:

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.

rna-seq • 363 views
ADD COMMENTlink modified 8 months ago by michael.ante3.2k • written 8 months ago by pixie@bioinfo1.4k
3
gravatar for michael.ante
8 months ago by
michael.ante3.2k
Austria/Vienna
michael.ante3.2k wrote:

Hi Pixie,

There are some tools available:

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

Cheers,

Michael

ADD COMMENTlink written 8 months ago by michael.ante3.2k

Thanks Michael, I will check those out!

ADD REPLYlink written 8 months ago by pixie@bioinfo1.4k
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