Hi,
I'm a new member and I have some questions about Illumina Pipeline GAII.
In Ilumina pipeline documentation there is no documentation about script used by the pipeline. Output of the pipeline show that Goat call different scripts. Does anyone have the details of call script process? What do each script? What is output of each script?...
When I run GERALD as a standalone program with parallelization, I have warning message like 'Warning: did not find any sequences to process (raw)' or 'Warning: none of 25092 data sequences passed filter criteria '(($F[5]>=0.6))' at /env/borneo/pipeline/GAPipeline-1.0/Gerald/qualityFilter.pl line 231.' Does anyone deals with this warning? In this output the lane_tile process are not in order. Does anyone know why? Is it due to the parallelization? This is a problem for me to determine what is the lane_tile concern by this warning.
Last, I would like understand ELAND algorithm. But I didn't find any documentation. Somebody know how can I get this information? saw in documentation that ELAND make several pass alignements. I would like more explanations about the alignment process : pass, error rate...
Thanks
I'm a new member and I have some questions about Illumina Pipeline GAII.
In Ilumina pipeline documentation there is no documentation about script used by the pipeline. Output of the pipeline show that Goat call different scripts. Does anyone have the details of call script process? What do each script? What is output of each script?...
When I run GERALD as a standalone program with parallelization, I have warning message like 'Warning: did not find any sequences to process (raw)' or 'Warning: none of 25092 data sequences passed filter criteria '(($F[5]>=0.6))' at /env/borneo/pipeline/GAPipeline-1.0/Gerald/qualityFilter.pl line 231.' Does anyone deals with this warning? In this output the lane_tile process are not in order. Does anyone know why? Is it due to the parallelization? This is a problem for me to determine what is the lane_tile concern by this warning.
Last, I would like understand ELAND algorithm. But I didn't find any documentation. Somebody know how can I get this information? saw in documentation that ELAND make several pass alignements. I would like more explanations about the alignment process : pass, error rate...
Thanks
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