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Old 06-09-2011, 09:52 AM   #1
arrchi
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Default cufflinks without a reference stuck at chrM

My code is as simple as this:
Code:
cufflinks -o test accepted_hits.bam
The bam file was generated by tophat. Both tophat and Cufflink are the latest version (1.3 and 1.03).

Without a reference, cufflinks stop and here is the last output:

Quote:
Processing Locus chr9:141152985-141153035 [***************** ]> Processing Locus chrM:0-16571 [************************ ] 97%
I tried cufflinks (v 1.0.2). I saw the same problem.

However, if I use cufflinks with a reference, the program runs smoothly without this problem.

Any suggestion?

Thanks in advance.

Last edited by arrchi; 06-09-2011 at 10:14 AM.
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Old 06-09-2011, 09:58 AM   #2
arrchi
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I checked cufflinks output , there is no chrX, chrY and chrM in the three output files. But my input bam file does have these three chromosome info.

Any ideas? please!

Last edited by arrchi; 06-09-2011 at 10:15 AM.
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Old 06-10-2011, 05:48 AM   #3
arrchi
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One of my several cufflinks programs does finished after stuck at chrM for about one day. So i guess it just needs a little bit more time and patience.
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Old 06-12-2011, 11:31 PM   #4
steven
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OK, that's probably because chrM is often overloaded with reads
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Old 01-27-2016, 08:40 PM   #5
baritone
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Default The problem is still there

And I'm posting this in the year of 2016
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Old 01-28-2016, 01:08 AM   #6
GenoMax
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Quote:
Originally Posted by baritone View Post
And I'm posting this in the year of 2016
Even with latest cufflinks version?
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