Dear all,
I do not mean to cross post, but maybe starting a new thread will help to solve this issue.
I read some posts from Bioinformatics section searching for a solution to an issue I'm suffering while using Cufflinks. I try to run it on a series of tophat bam files obtained from an alignment to the Rattus norvegicus reference genome (rn4).
Cufflinks hangs at 80% of the first analysis step while trying to match a result against the ChrUn reference:
"Inspecting bundle chrUn:427619-427681 with 20 reads"
It stays there for hours as if the program was running, but doesn't do anything...
I've produced a "ChrUn free" bowtie index in order to avoid this bug, but it still gets stuck at the same reads group.
Can somebody please tell me how to avoid this error or how to solve it? Has this (or any other equivalent issue) been a common problem anyone else encountered? Any solution or advice?
Thanks in advance.
JL
I do not mean to cross post, but maybe starting a new thread will help to solve this issue.
I read some posts from Bioinformatics section searching for a solution to an issue I'm suffering while using Cufflinks. I try to run it on a series of tophat bam files obtained from an alignment to the Rattus norvegicus reference genome (rn4).
Cufflinks hangs at 80% of the first analysis step while trying to match a result against the ChrUn reference:
"Inspecting bundle chrUn:427619-427681 with 20 reads"
It stays there for hours as if the program was running, but doesn't do anything...
I've produced a "ChrUn free" bowtie index in order to avoid this bug, but it still gets stuck at the same reads group.
Can somebody please tell me how to avoid this error or how to solve it? Has this (or any other equivalent issue) been a common problem anyone else encountered? Any solution or advice?
Thanks in advance.
JL
Comment