SOLiD data analysis with lifescope

[lre1234]

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..

[caspian]

Hi,

I'm not sure if you received a response to this question elsewhere. You can contact Life Tech's bioinformatics support for help with this specific issue. To contact:

ngs-amsupport
at
lifetech <period> com

[colindaven]

You can convert XSQ files to .csfasta and .qual with the
convertFromXSQ.sh script available from LifeTech.

eg
/usr/local/bin/XSQ_Tools/convertFromXSQ.sh -c lane1/5500xl_xxxxxx.xsq &

[mbblack]

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..

Given that one set of XSQ files worked and the other does not, my first suspect would indeed be the XSQ files themselves. Did you try just re-copying those files that failed over to your lifescope installation?

I use LifeScope 2.5.1 and have had no problems with it, even with a ridiculously complicated barcoded experiment (96 barcodes used, and all loaded on all 6 lanes). We run LifeScope on a Penguin cluster though, not a single workstation.

However, given that one set of files completed the run successfully, it would not seem to be an issue with your installation nor your hardware resources for the analysis. So I would first check those files (if both files are on Linux boxes, check the MD5 checksums with md5sum).

P.S. for what it is worth, my experience has been that for mapping color space reads in color space, LifeScope will actually give you the best results, relative to the couple of other tools I've tried with our data.