Question: cufflinks: nonsense gene merge error
0
gravatar for mtw
4.9 years ago by
mtw20
Vienna, Austria
mtw20 wrote:

Dear All,

cufflinks 2.2.1 produces tons of warnings related to 'max_gene_length' for an Arabidopsis data set and finally quits with the following message in the error log:

[...]
Warning: hit is longer than max_gene_length, skipping
Warning: hit is longer than max_gene_length, skipping
Error: nonsense gene merge - product > max_gene_length

My command line was:
cufflinks -q -p 30 --max-bundle-length 7000 --min-frags-per-transfrag 10 -o cuffout_denovo_D2_R2 ./D2_
R2.complete.cuff.bam

Interestingly, I only get this error for some replicates, while for others the tool runs through.

I could not find any reference to  'max_gene_length'  or 'nonsense gene merge' in the cufflinks manual, hence any hints are highly appreciated.

Cheers,
mtw
 

 

rna-seq • 1.1k views
ADD COMMENTlink modified 4.9 years ago by Sukhdeep Singh9.7k • written 4.9 years ago by mtw20
0
gravatar for Sukhdeep Singh
4.9 years ago by
Sukhdeep Singh9.7k
Netherlands
Sukhdeep Singh9.7k wrote:

I would suggest trying checking the fastq file for error (CIgar etc.)

Use this perl script by Simon on raw file 
http://seqanswers.com/forums/showpost.php?p=29075&postcount=8

Try running again, if exists, read the post below and try again 
http://seqanswers.com/forums/showthread.php?t=6183
 

ADD COMMENTlink written 4.9 years ago by Sukhdeep Singh9.7k
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