Question: Where is fastqselect in MIRA?
0
gravatar for Benn
8 months ago by
Benn7.9k
Netherlands
Benn7.9k wrote:

Hey,

I used to have a tool called fastqselect, it came with mira. I used it years ago (seen it in an old script). I would like to use it again, but in the meantime I have an other computer and different version of mira. But I can't find it on the new version anymore. Anyone know what happened? Or where I can find the tool solo? Thanks.

Ben

mira fastqselect • 141 views
ADD COMMENTlink written 8 months ago by Benn7.9k
2
gravatar for genomax
8 months ago by
genomax78k
United States
genomax78k wrote:
  1. You could use filterbyname.sh tool from BBMap suite.

    Description: Filters reads by name.

    Usage: filterbyname.sh in=<file> in2=<file2> out=<outfile> out2=<outfile2> names=<string,string,string> include=<t f="">

    names can be a file with one identifier per line.

  2. Peter Cock has: https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id

  3. fastqselect is in an old release of mira (https://launchpad.net/ubuntu/+archive/primary/+sourcefiles/mira/3.4.0.1-1/mira_3.4.0.1.orig.tar.bz2 ).

ADD COMMENTlink modified 8 months ago • written 8 months ago by genomax78k

Thanks man, do you know if that tool works with space in the names?

ADD REPLYlink written 8 months ago by Benn7.9k

BBTools generally leave spaces in names alone/carry them forward as is, so it should.

ADD REPLYlink modified 8 months ago • written 8 months ago by genomax78k

Thanks for additional point 3! Try that first.

ADD REPLYlink written 8 months ago by Benn7.9k
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