[Galaxy-france] Disable seeding in BWA using Galaxy

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[Galaxy-france] Disable seeding in BWA using Galaxy

Thierry Grange

Bonjour à tous

 

I would like to disable seeding when doing a sequence mapping using bwa. Apparently, this is commonly performed using the aln –l option set at a value higher than the read length, and is often set at values above 1000. In Galaxy, the default option is -1 for this parameter, and it is indicated that -1 corresponds to infinity. Does that mean that seeding can be disabled using -1, and that it is disabled by default on Galaxy? I don’t obtain exactly the same thing using -1 or 16000 for this parameter, even though the difference is marginal.

 

Thanks for your insights

 

 

Thierry

Institut Jacques MONOD

Paris

 


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