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Old 07-24-2012, 05:31 AM   #1
Jluis
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Location: Bilbao

Join Date: Apr 2012
Posts: 44
Default Cufflinks gets stuck at chrUm fron (rat) rn4 mapping

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

Last edited by Jluis; 07-24-2012 at 06:08 AM. Reason: ortography
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Old 12-21-2012, 11:40 AM   #2
caballien
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Location: pittsburgh, pa

Join Date: Nov 2012
Posts: 7
Default

I have a similar problem now, did you find a solution?
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Old 01-01-2013, 11:29 PM   #3
Jluis
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Location: Bilbao

Join Date: Apr 2012
Posts: 44
Default

@caballien

I had to clean my reference file (.gtf) getting rid of any "chrM" or "_random" line. To achieve this I used a very simple Perl script (I'm sure there are faster ways to do it using bash, but ...)
Code:
#!usr/bin/perl
use strict;
use warnings;
use Getopt::Long;
#usage example:perl /path_to/chrM_cleaner.pl -r /path_to/file.gtf

my ( $in);
GetOptions(
    'reference=s'     => \$in,
     );

print "$in \n";

open INFILE, '<',  "$in" or die ("Can't open INFILE ERROR: $!\n");
#open a modified reference file to write
open OUT, '>', "$in"."_2.gtf" or die ("Can't open OUTFILE ERROR: $!\n");

while (<INFILE>) {
      if ($_=~/chrM/){ next;}#skips chrM lines

      elsif ($_=~/_random/){next;}#skips chr _random lines

      else{
	    chomp($_);
            print OUT "$_\n";#prints the other lines to the modified reference file
      }
}
I hope this works for you also...
I'm very sorry for this delay in answering...
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