Question: Cufflinks Not Able To Assemble Transcripts In High Read Coverage
gravatar for Abhi
9.1 years ago by
United States
Abhi1.5k wrote:

Hey Guys

I am using cufflinks for building transcriptome. I am seeing some regions where in-silico model predictions is re-affirmed by RNA-Seq data but however cufflinks or scripture is not able to assemble a transcript.

Is there anything that we can do to improve the sensitivity of cufflinks.

Here is a snapshot of on such example.

IGV Snapshot

Thanks! -Abhi

cufflinks rna transcriptome • 3.4k views
ADD COMMENTlink modified 7.0 years ago by Biostar ♦♦ 20 • written 9.1 years ago by Abhi1.5k

This might has been fixed in the most current release. This is from the cufflinks web site:

1.2.1 release - 11/30/2011 This release fixes an issue introduced with version 1.2.0, where a very deeply sequenced locus could cause Cufflinks or Cuffdiff to assign 0 FPKM to subsequent genes. It also corrects a bug where Cufflinks wasn't reporting very deeply sequenced loci as HIDATA.

ADD REPLYlink written 9.0 years ago by Pascal160

Can you be more specific on "cufflinks or scripture is not able to assemble a transcript"?

ADD REPLYlink written 9.1 years ago by Peter Kovac70

@Peter : I guess what I wanted to say was that during the trasncriptome reconstruction by cufflinks it is not able to assemble a transcript in a region where there are lot of reads and splicing event taking place which indicates a plausible transcript. Also the gene model has a predicted gene in that region -Abhi

ADD REPLYlink written 9.1 years ago by Abhi1.5k
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