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Old 03-17-2015, 04:36 PM   #12
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Hi Rod,

There is currently no way to fix that. I specifically made it that way to replicate the name structure of real Illumina reads. For paired reads, many tools or formats (such as sam) require both to have exactly matching names, excluding anything after the first whitespace (such as a 1 or 2). Most aligners, therefore, trim everything after the first whitespace, though with BBMap you can disable this with the "keepnames" flag.

What are you doing that requires no space? I could add an option for that, but I'm interested in why.
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