Cuffmerge: skipping large bundles error

Question

[RoryC]

Hey everyone,

I've seen lots of similar questions to this one asked before so apologies, but not one specifically for Cuffmerge rather than Cufflinks. When originally running Cufflinks I was getting error messages such as:

N00001:11202239-15247668 Warning: Skipping large bundle.

I avoided this however by adding --max-bundle-length 10000000 to my Cufflinks command. However now when I run Cuffmerge on the resulting transcript GTFs (from 5 individuals, 6 tissues), these errors start reappearing, even though those regions are resolved in the Cufflinks output. As Cuffmerge has no max-bundle-length option, I'm not sure how to fix this, anyone encountered a similar problem?

Cheers, Rory

[RoryC]

As an update, these errors don't occur if the -g option for using a genome annotation GTF is not used. Looking at the annotation file I can't see any genes spanning more than 3.5Mb in these regions, so no idea why this is happening. Anyone know how cuffmerge uses the GTF file? This affects about 1/3 of my 1Gb genome so it's a pretty major fault, could be something wrong with the data itself.