Question: What Does The Error "Warning: Skipping Large Bundle." Mean In Cufflinks?
1
gravatar for Sameet
7.2 years ago by
Sameet290
Sameet290 wrote:

Is there any way around this error?

cufflinks • 2.4k views
ADD COMMENTlink written 7.2 years ago by Sameet290
3
gravatar for Malachi Griffith
7.2 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith17k wrote:

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.

ADD COMMENTlink written 7.2 years ago by Malachi Griffith17k

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.

ADD REPLYlink written 7.2 years ago by Sameet290
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