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Old 01-06-2012, 09:08 AM   #4
dmacmillan
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Location: British Columbia

Join Date: Jan 2012
Posts: 49
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Unfortunately the error message was buried in the command line after "vi"ing into the bam2windows.pl to see the line that was causing the issue. What I said earlier was fairly close to the output, but since I am using very large .bam files it will take at least another day to run the code on them again.

As you probably figured from above I am running linux, specifically centOS 2.16.0
Perl version v5.8.8 built for x86_64-linux-thread-multi

The exact command I used was as follows:
perl bam2windows.pl /projects/MYUSERNAME/DLBCL/CNV/RG065/tumour/A01419_9_lanes_dupsFlagged.bam /projects/MYUSERNAME/DLBCL/CNV/RG065/normal/A01440_8_lanes_dupsFlagged.bam > A01419.tab

Note that these are actually LINKS to the bam files and not the bam files themselves. I discovered this afterwards and I am currently testing them on the included .bam files that were supplied.

I'll let you know how it goes, thanks for the very prompt response!

-cheers
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