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  • Filter Illumina reads & maintain PE ordering

    Can anyone recommend a tool to filter my paired end Illumina reads (something like mean Q score), either shuffled together in the same file or in separate files, while maintaining the read order? i.e if 1 read of a pair fails, remove it's mate as well (and preferably stick it in a singlets file or something)? I'm aware of the Galaxy web tool but don't want to upload gigs and gigs of sequence data...

    Thanks in advance!

  • #2
    This thread might help. I've been using fastx to filter read1.fq and read2.fq and then the script provided in the thread to make a file of orphaned reads and a read1 and read2 correctly-paired set of files that can then optionally be interleaved. Hopefully tools like fastx can be updated to handle paired-end data out of the box (so to speak) but for now, this works well.

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    • #3
      Thanks.. I didn't even realize galaxy used the fastx tools. I've only ever found the page for the web interface with no mention of the software.

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