Lilach: This tool works on unaligned reads in fastq format before they are mapped. It is useful for merging mates together into a single read for QC processing, filtering, and trimming. Thanks! anton On Wed, Sep 11, 2013 at 4:34 AM, lilach noy <lilachnoy@gmail.com> wrote:

Hi all,

Has anyone used FASTQ joiner with a file containing multi-mapped reads? I'm pretty sure i have reads mapped to several locations and i don't know what this tool does with it? will it locate the right map according to the paired read? will it use the first read location and ignore the rest or maybe it will exclude all multi-mapped reads prior to paring?

Regards, Lilach

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