Hi all,
I am trying to map some barcoded exome data sets that was generated on the SOLiD 5500. I have the XSQ files and am using Life Techs lifescope software, but have run into a problem. While aligning the progress gets to about 50% completed then freezes and does not proceed past that point. The software itself is not crashing as I can still use it, but the analysis seems to stop. If I look at the log files, no new information gets written to the files.
I'm not sure if there is a problem with my files. could they be corrupted in some way? Is there anyway to possible check for this? I should mention that other set of samples, that came off the machine at the same time went through the analysis pipeline just fine.
I am just using lifescope to align the data, then either samtools or GATK for SNP/indel calling. I know that BWA won't work with the XSQ file format, are there any other applications that can work with this data. It seems very specific to the SOLiD and limits what can be done with it.
Thanks for you help..
I am trying to map some barcoded exome data sets that was generated on the SOLiD 5500. I have the XSQ files and am using Life Techs lifescope software, but have run into a problem. While aligning the progress gets to about 50% completed then freezes and does not proceed past that point. The software itself is not crashing as I can still use it, but the analysis seems to stop. If I look at the log files, no new information gets written to the files.
I'm not sure if there is a problem with my files. could they be corrupted in some way? Is there anyway to possible check for this? I should mention that other set of samples, that came off the machine at the same time went through the analysis pipeline just fine.
I am just using lifescope to align the data, then either samtools or GATK for SNP/indel calling. I know that BWA won't work with the XSQ file format, are there any other applications that can work with this data. It seems very specific to the SOLiD and limits what can be done with it.
Thanks for you help..
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