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Cufflinks, Warning: Skipping Large Bundle

I am trying to analyze mouse RNA-seq expression data but am getting the following error during cuffmerge:

8:119910359-124345724 Warning: Skipping large bundle

I'm using Ensemble m38.69 (Accession #GCA_000001635.2). It seems that there is a giant gene annotated in that interval, GM20388. I understand that the default bundle size in cufflinks (I'm using v2.0.2) is 3,500,000 so I tried increasing the bundle size using the following command:

--max-bundle-length 8000000

Even with the bundle length increased to 8,000,000 I am still getting the same "Skipping large bundle" error. The entire cufflinks command is shown here:

cufflinks --max-bundle-length 8000000 -u -b Mus_musculus.GRCm38.69.dna.toplevel.fa -p 11 -o cufflinks_out/Sample10831 tophat_out/Sample10831/accepted_hits.bam

Any thoughts as to why I'm still getting the error?

Thanks!!

cuffmerge rna-seq cufflinks
• 5,922 views • link
updated by Istvan Albert Istvan Albert • written by buchnerd buchnerd

may be increase more, also check this post

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written by Sukhi Singh Sukhi Singh

Tried increasing to a bundle size of 100,000,000 and then 10,000,000,000. Neither one worked.

• 0 views • link
written by buchnerd buchnerd

did you determine how to fix this error? I got the exact same problem in this genome coordinate.

• 1 views • link
written by thefinitemachine • thefinitemachine

Nope, haven't figured it out. Increasing the bundle size didn't seem to work.

• 1 views • link
written by buchnerd buchnerd

1 answer

As Sukhdeep says keep increasing it to even larger values.

• 3 views • link
written by Istvan Albert Istvan Albert

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