Question: How to generate FPKM values for Velvet/Oases assembled transcripts
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gravatar for upendrakumar.devisetty
4.3 years ago by
United States
upendrakumar.devisetty350 wrote:

Hi,

Can anyone point to me of how i can generate FPKM values for the Velvet/Oases assembled transcripts. I know TopHat/Cufflinks pipeline for generating FPKM values but in this case i already have Velvet/Oases assembled transcripts along with the reads. All i want to do is to see the expression levels of Velvet/Oases assembled transcripts. Any help is appreciated.

rna-seq velvet/oases fpkm • 1.3k views
ADD COMMENTlink modified 4.2 years ago by Biostar ♦♦ 20 • written 4.3 years ago by upendrakumar.devisetty350

So you don't have reads, or you have reads as well as transcripts?

ADD REPLYlink written 4.3 years ago by RamRS21k

I have both reads and transcripts

ADD REPLYlink written 4.3 years ago by upendrakumar.devisetty350

Thank you for the clarification - I've modified your question to reflect this.

ADD REPLYlink written 4.3 years ago by RamRS21k

Thanks for the modification. Appreciated

ADD REPLYlink written 4.3 years ago by upendrakumar.devisetty350

I think you can still use your transcripts (in gtf format) with cufflinks to measure expression. Just provide transcripts file as reference annotation.

 -G/--GTF                     quantitate against reference transcript annotations
ADD REPLYlink written 4.3 years ago by poisonAlien2.8k

Good point. I have the transcripts in bed format and probably can change them to gtf and use them but how about the bam file (accepted_hits.bam) file that is need as input with cufflinks ? Do you think i should map all the reads from which i generated transcripts from using TopHat and then run cufflinks? Please advise

ADD REPLYlink written 4.3 years ago by upendrakumar.devisetty350

No need to align again. Just us the same bam file which was used to generate the tx annotation file.

ADD REPLYlink written 4.3 years ago by poisonAlien2.8k
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