Question: Where is fastqselect in MIRA?
0
gravatar for Benn
19 days ago by
Benn7.1k
Netherlands
Benn7.1k 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 • 66 views
ADD COMMENTlink written 19 days ago by Benn7.1k
2
gravatar for genomax
19 days ago by
genomax69k
United States
genomax69k 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 19 days ago • written 19 days ago by genomax69k

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

ADD REPLYlink written 19 days ago by Benn7.1k

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

ADD REPLYlink modified 19 days ago • written 19 days ago by genomax69k

Thanks for additional point 3! Try that first.

ADD REPLYlink written 19 days ago by Benn7.1k
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