[galaxy-user] LASTZ: Controlling Length of Hits

Bossers, Alex Alex.Bossers at wur.nl
Tue Mar 22 11:30:04 EDT 2011


Hi
there is an example in the windshield splatter analysis using galaxy where for metagenomics they filter their data on hit length related to the initial individual subject sequence length in megablast.
In simple steps (from memory so don't shoot me :) ) all in galaxy assuming fasta input;
1) upload fasta
2) compute sequence lengths on 1
3) on set 1 perform megablast (or whatever) that give a hit length
4) combine 2 and 3 on basis of unique seqname
5) use the filter tool to filter on hitlngth collumn divided by original length collumn (in the example > 50% hitlength)
6) strip additional collumns of length to return a valid megablast or lastZ file....

You can save the history as a workflow for repetive use.

something like this you were looking for?

The video is in the screencasts sections using 454 data and megabast...but it looks similar to your question...

Alex

________________________________________
Van: galaxy-user-bounces at lists.bx.psu.edu [galaxy-user-bounces at lists.bx.psu.edu] namens Bob Harris [rsharris at bx.psu.edu]
Verzonden: maandag 21 maart 2011 22:04
Aan: JASON G. BANKERT
CC: galaxy-user at bx.psu.edu
Onderwerp: Re: [galaxy-user] LASTZ: Controlling Length of Hits

On Mar 21, 2011, at 1:45 PM, JASON G. BANKERT wrote:
> We're trying to only get hits of certain lengths.  Is there a
> setting to use that sets the minimum length for each hit?

Howdy, Jason,

Lastz (the underlying program) has some options that are geared toward
filtering by length, though none uses length exactly.  In the lastz
wrapper for galaxy, the only length-relevant filtering option is "Do
not report matches that cover less than this percentage of each
read".  If your reads are all the same length, or close to the same
length, this could meet your needs.  If the length distribution of
your reads is pretty wide (as can occur with 454), then probably not.

I'm not familiar with all the rest of the galaxy toolset, but it seems
like there's bound to be a tool that can compute interval length from
the interval's start and end, and then filter on that.

Bob H


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