gsMapper failed to create ace or bam file

dnajuice · 08-23-2012, 12:22 PM

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!

jimmybee · 08-23-2012, 05:01 PM

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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08-23-2012, 12:22 PM	#1
dnajuice Junior Member Location: USA Join Date: Aug 2012 Posts: 8	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!

08-23-2012, 05:01 PM	#2
jimmybee Senior Member Location: Adelaide, Australia Join Date: Sep 2010 Posts: 119	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