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Old 09-08-2014, 02:00 PM   #33
biodan
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Location: NYC

Join Date: Oct 2012
Posts: 2
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Thanks for the tip Brian. The files are indeed pairs, the 'clean' files were generated by trimming the adapters (commands shown below) from parent files which have been previously, successfully mapped by Bowtie2 without adapter trimming.

/opt/bbmap/bbduk.sh -Xmx1g in=mrg_1g_C10_R1.fastq.gz out=clean_1g_C10_R1.fastq.gz ref=/opt/bbmap/resources/nextera.fa.gz ktrim=rl hdist=1

/opt/bbmap/bbduk.sh -Xmx1g in=mrg_1g_C10_R2.fastq.gz out=clean_1g_C10_R2.fastq.gz ref=/opt/bbmap/resources/nextera.fa.gz ktrim=rl hdist=1

In any event, your repair.sh script fixed the files.
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