cufflinks: nonsense gene merge error

Question

[mtw]

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

Answer 1

[Sukhi Singh]

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