bfast localalign -U option?

Protaeus · 09-17-2010, 10:13 AM

Hello,

What are the downsides of using the -U option at the bfast localalign step? I presume it'll be more computationally expensive, but are there things with the resulting data that would be of concern?

nilshomer · 09-17-2010, 12:11 PM

Quote:

Originally Posted by Protaeus

Hello,

What are the downsides of using the -U option at the bfast localalign step? I presume it'll be more computationally expensive, but are there things with the resulting data that would be of concern?

When not using the '-U', bfast enforces that where the seeds/masks match the reference during 'bfast match' also match the reference in the final alignment. This is a constrained Smith Waterman alignment, which speeds up the local alignment. Using the '-U' option ignores those constraints.

The philosophical question that the '-U' option lets one ask is if we get to a 100bp window in a 3Gb genome, should we constrain the alignment based on how we got there?

Protaeus · 09-17-2010, 12:50 PM

That brings up a separate but related question I had. A lot of my recent illumina runs have been 101bp on bacterial genomes. Generally speaking, the key width for my indexes is 30. Would there be any reason to believe I would benefit from trying a larger key width? Or is this where the -U option in localalign might be helpful?

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09-17-2010, 10:13 AM	#1
Protaeus Member Location: 86001 Join Date: Aug 2010 Posts: 21	bfast localalign -U option? Hello, What are the downsides of using the -U option at the bfast localalign step? I presume it'll be more computationally expensive, but are there things with the resulting data that would be of concern?

09-17-2010, 12:50 PM	#3
Protaeus Member Location: 86001 Join Date: Aug 2010 Posts: 21	That brings up a separate but related question I had. A lot of my recent illumina runs have been 101bp on bacterial genomes. Generally speaking, the key width for my indexes is 30. Would there be any reason to believe I would benefit from trying a larger key width? Or is this where the -U option in localalign might be helpful?