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Old 01-23-2017, 01:18 AM   #39
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,479

Feature request: It'd be quite nice to be able to write marked duplicates to a different file or files. At the moment, I have to mark duplicates and write everything to a temporary file, which is then processed. Granted, one CAN use "out=stderr.fastq" and send that to a pipe, but then one needs to deal with all of the normal stuff that's written to stderr.

The impetus behind this is removing optical duplicates before delivery to the our labs but still writing them to a separate file or files in case they need them for some reason.

BTW, do you have any recommendations for the "dist" parameter on a HiSeq 4000? I was planning to just do a parameter sweep, but if that's already been done by someone else...
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