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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