Hello Thierry,

Yes, to set the job parameters with no seeding, using the default setting for this parameter ("-1", aka infinity) is a standard method.

If you read what people are doing, they are split into two camps. Some go with the default (infinity). Some go with really high -l value, 10k or so. Both are producing results in publication analysis. I think the choice is yours.

Take care,

Jen
Galaxy team
On 2/18/14 8:36 AM, Thierry Grange wrote:

Hello

 

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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