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?