Where is fastqselect in MIRA?

Question

[Benn]

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

Answer 1

[GenoMax]

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 ).

[Benn]

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

[GenoMax]

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

[Benn]

Thanks for additional point 3! Try that first.