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Old 08-23-2012, 11:22 AM   #1
dnajuice
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Location: USA

Join Date: Aug 2012
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Default gsMapper failed to create ace or bam file

Hi,

I encountered a problem with gsMapper (v2.6) when I tried to align 10M Illumina paired end reads on to 100 large contigs. Even though I set the parameters to output file in ACE and BAM format, neither was generated. Can anybody give me a clue?

Also, is there any way to use the gsMapper output files to generate scaffolds based on paired end information?

Thanks!
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Old 08-23-2012, 04:01 PM   #2
jimmybee
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Why are you using gsMapper with Illumina data? Its a GSFLX tool, so I would have thought it would be much easier to use programs designed to work with smaller reads and Illumina tech
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