Cufflinks, Warning: Skipping Large Bundle

Question

[buchnerd]

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!!

[Sukhi Singh]

may be increase more, also check this post

[buchnerd]

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

[thefinitemachine]

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

[buchnerd]

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

Answer 1

[Istvan Albert]

As Sukhdeep says keep increasing it to even larger values.