Cufflinks Not Able To Assemble Transcripts In High Read Coverage

Question

[Abhi]

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.

Thanks! -Abhi

[Pascal]

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.

[Peter Kovac]

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

[Abhi]

@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