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Old 03-19-2008, 11:51 AM   #1
bioinfosm
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Default New version of Solexa GA pipeline tool

Any help summarizing the changes from previous release? I cant seem to find a change log sort of thing

A discussion would be helpful to all ... the _export format looks useful, and so does usage of multiple fasta files as reference


There is a new MAQ out as well... spring time !

Last edited by bioinfosm; 03-21-2008 at 01:37 PM.
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Old 03-26-2008, 09:13 AM   #2
bioinfosm
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Default

Ok, I have done some analysis looking at the same Image data with both versions:

The new pipeline generates more clusters (100-1000 more per tile), has higher %PF clusters values, lower error rates (approx 0.2% lower), lower first cycle intensity (400-800 points lesser) and comparable %PF Align and % Intensity after the 20th cycle.

All these comparisons were done from the summary.htm file that gets generated from the run. I used the same offsets file for the goat pipeline.
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Old 05-28-2008, 07:51 AM   #3
bioinfosm
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Default Using SGE grid for GA pipeline

Hi,

Any custom experience using the SGE for parallel execution of the entire pipeline run. The manual explains the make files, checkpoints and hooks, but does not tie them together into something that can be readily used.

Here is some more info, but not complete
http://www.genographia.org/portal/to...uster-software

Anyone already using the SGE grid to run the pipeline and eland .. and free to share any caveats or job submission script that can be customized and used?

thanks....
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