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Old 01-22-2012, 04:08 PM   #1
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Location: Sydney

Join Date: Feb 2011
Posts: 149
Default what files are produced from CNVnator ?


I'm wondering if anyone can let me know what outputs to expect from CNVnator for each step.
I've followed the instructions in the readme file, and except for the last step (-view), calculations appear to proceed without any errors. Only 1 file is being created and updated - the .root file. Are there supposed to be any other directories or files?

When i run the last command (-view), it says it can't find the 'bin' directories or the read depth histogram. These are indeed not in the working directory.

I've asked the author but didn't get any reply.

background: it might be that my inputs are not correct. I'm trying to run this on a .bam file from an alignment of 100 PE reads to a 12kb scaffold/reference. A total of 4291024 reads were placed.

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Old 01-23-2012, 08:14 AM   #2
Location: British Columbia

Join Date: Jan 2012
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If you generate a histogram you are asked to input the bin size, therefore you will only be able to view a histogram of that particular size. I believe you must also go through signal partitioning before viewing.
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