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Old 04-22-2010, 04:08 PM   #1
bbimber
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Default Mosaik: possible for MosaikText to create SAM or BAM, but not compress it?

MosaikText can convert a mosaik output into either SAM or BAM files; however, it always produces a zipped output. Is there a way to make it produce one of these formats without gzipping it?
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Old 04-22-2010, 09:21 PM   #2
bbimber
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correction: the BAM file produced my mosaik can be used as is.
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Old 05-20-2010, 03:59 PM   #3
guisinmm
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Default Gambit crashes with .bam file from Mosaik

The visualization software Gambit crashes when I attempt to open my .bam file created using Mosaik (MosaikText). Does anyone else have this problem? I am able to open the .ace file using consed, but I'd like to try Gambit.
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Old 05-27-2010, 07:59 AM   #4
kraigrs
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I recently used MOSAIK to align my short Illumina reads and had the -m unique parameter initialized, but when I convert the map file to .sam format, I see reads that aligned to multiple places. Does anyone understand this?
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