Question: Fused Or Not Fused Gene
0
gravatar for upendrakumar.devisetty
7.4 years ago by
United States
upendrakumar.devisetty360 wrote:

Does anybody know of how to tell from tophat/cufflinks output that whether or not a transcript is fused or not compared to gff annotation (reference annotation)?

After looking at the tophat bam file and transcript.gtf along with gff (reference) file on IGV i found that some of the annotated genes are fused and some are not fused (i.e a single gene in transcript.gtf is reported as two genes in reference gff and sometimes a fused gene (2 genes) in transcript.gtf is reported as single gene in reference gff). All i want to know is how many of these discrepencies exist in reference annotation (gff) compared to cufflink transcripts.

Any ideas?

fusion cufflinks • 2.1k views
ADD COMMENTlink modified 6.2 years ago by Biostar ♦♦ 20 • written 7.4 years ago by upendrakumar.devisetty360

Have you tried running tophat fusion to answer the question more directly?

ADD REPLYlink written 7.4 years ago by Sean Davis26k

No i haven't. That will be my next plan to do if i can't get to use my current tophat/cufflinks output.

ADD REPLYlink written 7.4 years ago by upendrakumar.devisetty360

are you using -g or -G option? My guess is -G will avoid that kind of problems.

ADD REPLYlink written 7.4 years ago by JC9.6k

I haven't used either -g or -G with cufflinks because all i wanted to know is novel genes and transcripts.

ADD REPLYlink written 7.4 years ago by upendrakumar.devisetty360

you can use -g, Cufflinks will report the known models and novel isoforms/transcripts

ADD REPLYlink written 7.4 years ago by JC9.6k

Yes i just checked that one. I always thought -g would not produce novel isoforms/transcripts. But how does it solve my problem of detecting fusion genes in my RNAseq data compared to reference annotation?

ADD REPLYlink written 7.4 years ago by upendrakumar.devisetty360
1
gravatar for Sean Davis
7.4 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

Unless you use a workflow designed to detect fusions, you will not find them. If you mean readthrough events, those may be captured by tophat. You might want to look at cuffcompare to see if that meets your needs.

ADD COMMENTlink written 7.4 years ago by Sean Davis26k
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