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optimuscoprime / autoadapt

Automatic quality control for FASTQ sequencing files
GNU General Public License v2.0
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paired mode - keep 2 files in sync #2

Open drmjc opened 10 years ago

drmjc commented 10 years ago

Hi, when adaptor trimming on paired end data, its possible that 1 read will become too short and get discarded. If i'm not mistaken, its important that the remaining read from the pair in the other file get discarded too (or stored in another file) so that the paired read files stay in sync (same # reads in the same order). This is something that trimgalore attempts to do (though in my hands trim galore keeps on creating corrupt fq.gz files)...

optimuscoprime commented 10 years ago

Good point, I think we handle this already (by running cutadapt twice with special arguments to handle paired-end data), but let me know if you have found a bug with it :)