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Old 12-24-2014, 07:49 PM   #99
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,138
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Basically something like this:

Code:
$ replace_windows_OS_specific_bbduk_command_here -Xmx2g in1=/path/to/sample_R1.fastq in2=/path/to/sample_R2.fastq out1=/path/to/sample_R1_no_adapters.fastq out2=/path/to/sample_R2_no_adapters.fastq ref=/path/to/bbmap/resources/truseq.fa.gz ktrim=r [and other options for bbduk to follow]
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