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Old 09-08-2014, 02:31 PM   #34
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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I'm glad that repair.sh worked for you. In the future, I suggest running paired files simultaneously when doing any sort of trimming/filtering, like this:

bbduk.sh -Xmx1g in1=mrg_1g_C10_R1.fastq.gz in2=mrg_1g_C10_R2.fastq.gz out1=clean1.fastq.gz out2=clean2.fastq.gz ref=/opt/bbmap/resources/nextera.fa.gz ktrim=r hdist=1

That way, pairs will be kept together throughout the pipeline.
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