Question: How to derive sequence of novel transcript identified by Cufflinks
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gravatar for CY
5 months ago by
CY560
United States
CY560 wrote:

I am new to transcript level analysis using RNA-Seq. The goal is to retrieve sequence of newly identified transcript from RNA-Seq data. We just finished runing Cufflinks and seems like that a number of putative novel transcripts were generated. What do I have to do to further retrieve the sequence of novel transcript? Or at least recognize the exons included in novel transcripts? Thanks

rna-seq transcript • 170 views
ADD COMMENTlink written 5 months ago by CY560

do you have a reference transcriptome/genome at your disposal?

ADD REPLYlink written 5 months ago by lieven.sterck10.0k

Yes, it is reference guided.

ADD REPLYlink written 5 months ago by CY560

in that case you can align your reads to the reference and then subtract all the ones that align to known genes and the leftover are the novel ones.

or is this not what you're asking for?

ADD REPLYlink written 5 months ago by lieven.sterck10.0k
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