Keep large paired-end Fastq datasets in sync

[sklages]

Hi Folks,

probably a common situation.

Having a Illumina PE dataset (qseq converted to fastq), I'd like to
remove some adapter sequences or clip low quality ends (e.g. with
the fastX toolkit).

Usually I end up having a dataset where there's not always a mate/
counterpart of read1 in read2 fastq, because most tools usually don't
care about pairs. OK.

Are there tools available for e.g. filling dummy sequences in positions
where there is the mate/counterpart missing? Or vice versa, remove
the single read if there is no mate/counterpart?

Or do I have to write it on my own? I am just curious ..
Having a bunch of HiSeq lanes makes this task tedious ;-)

Sven

[maubp]

There are scripts out there to do this kind of thing, e.g. my "Divide FASTQ file into paired and unpaired reads" tool which comes with a wrapper for Galaxy, see http://community.g2.bx.psu.edu/ - in this case it takes a single mixed FASTQ file and works out the pairs based on the read names.

[sklages]

This tool is not found in the tools section, isn't it? I couldn't find it. Thanks.

[maubp]

It isn't part of the default install available at http://usegalaxy.org if that's what you mean. The Galaxy Tool Shed http://community.g2.bx.psu.edu/ is for people who have their own local Galaxy to add extra tools. As written this particular tool using the Galaxy library functions for file parsing, so it can't easily be used on its own. It could be modified to use Biopython for instance.

[sklages]

Ah, ok, now I got it ;-) Thanks.