Question: Disable Seeding Using Galaxy
gravatar for Thierry Grange
4.8 years ago by
Thierry Grange10 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
bwa alignment • 750 views
ADD COMMENTlink modified 4.8 years ago by Jennifer Hillman Jackson25k • written 4.8 years ago by Thierry Grange10
gravatar for Jennifer Hillman Jackson
4.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:
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 -- Jennifer Hillman-Jackson
ADD COMMENTlink written 4.8 years ago by Jennifer Hillman Jackson25k
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