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Old 07-27-2011, 07:09 PM   #1
Location: Beijing

Join Date: Jul 2011
Posts: 74
Default cufflinks error:Read Type: 0bp single-end

Dear all,

I use cufflink to map transcript, but the results "gtf" are empty.

The command I used :
cufflinks -o cufflinks_out -G Mus_musculus.NCBIM37.63.gtf aln-reliable.bam
and get:
Map Properties:
> Total Map Mass: 712614.00
> Read Type: 0bp single-end
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[09:59:53] Estimating transcript abundances.
> Processing Locus NT_166433:11954-18898 [************************ ] 99%段错误

I google the error, and find someone said it was the problem from the annotation file. So I download another mm9.gtf annotation file from Ensemble "Mus_musculus.NCBIM36.46.gtf". Still ,the same error.

Any thoughts? Thank you
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