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Old 08-03-2011, 12:20 AM   #1
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Location: Leiden, Netherlands

Join Date: Aug 2011
Posts: 1
Default maq indelpe does not give any results

Hello all!

I have a question about the command: maq indelpe. I am executing the command using:

maq indelpe maq indelpe /data/maqgene/genomes/elegans.bfa

But I fail to get results. The .map file is from a paired-end run and is generated using MaqGene. If however I use the command:

maq indelsoa maq indelpe /data/maqgene/genomes/elegans.bfa

it works fine, but I am more interested in the paired-end deletions. Of course it could be that there are no deletions detected, but how can I test if the indelpe call actually does what it should? In other words is there a test case or anything that I can use. Also does anyone know if the mapping file, because it was generated by MaqGene is maybe different which might cause problems?

Thanks for the help!

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