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Old 06-27-2017, 10:48 AM   #238
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Hi Ksenia,

This is always a tricky problem when people rename the reads. However, it looks like in your case the file is interleaved (that's my guess from the read headers), and thus you should only be using a single input to bbduk and add the "interleaved" flag, but it seems you are giving it two input files. Can you post the bbduk command, and explain exactly what came out of the SRA extraction process? Also, posting the SRA extraction command you use might help (it won't help me, but it might mean something to somebody).
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