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Old 03-05-2015, 05:41 AM   #2
super0925
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Location: UK

Join Date: Feb 2014
Posts: 206
Default Cufflinks/Cuffmerge/Cuffdiff error 'subsequence cannot be larger than 16338'

Hi all
I'm doing DE analysis on cow samples.
I use the reference genome of Ensembl UMD3.1, which I thought is the latest version.
However, when I ran Tophat2-Cuffdiff2 pipeline (default parameter setting), I still get this warning:


Warning: couldn't find fasta record for 'GJ058256.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'GJ058424.1'!
......



(1) What does it mean? Is it very trouble for my downstream analysis?

And if I ran Tophat2-Cufflinks/Cuffmerge-Cuffdiff2 ((default parameter setting)), I got the error:

Warning: couldn't find fasta record for 'GJ060129.1'!
This contig will not be bias corrected.

......

Error (GFaSeqGet): subsequence cannot be larger than 16338
Error getting subseq for TCONS_00062149 (1..16448)!


(2) Why could I get this result? How can I go on with Tophat2-Cufflinks/Cuffmerge-Cuffdiff2?


Thank you !

Last edited by super0925; 03-05-2015 at 07:40 AM.
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