What Does The Error "Warning: Skipping Large Bundle." Mean In Cufflinks?

Question

[Sameet]

Is there any way around this error?

Answer 1

[Malachi Griffith]

This question has been asked and answered on SeqAnswers: Default cufflinks, Warning: Skipping large bundle. You can also refer to the Cufflinks Manual. See the --max-bundle-length option which states that it determines:

Maximum genomic length allowed for a given bundle. The default is 3,500,000 bp.

A 'bundle' is the size of a genomic region that is expected to contain a single gene that is being observed by a read group assembled by Cufflinks.

[Sameet]

Thank you @malachig. I am working with a very small genome (about 15 MB). I do not understand how I can set a ball-park --max-bundle-length, i will start with 20 MB and see how it goes.