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Old 12-25-2014, 05:35 AM   #100
michaellim
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Location: England

Join Date: Dec 2014
Posts: 28
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Quote:
Originally Posted by GenoMax View Post
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]
Hi Genomax,

Sorry, but I don't understand what is "/path/to/", if my files are all in C: drive Windows, will it be

jave -ea -Xmx2g in1=C:\sequencing\ST131_1_R1.fastq in2=C:\sequencing\ST131_1_R2 out1=??? out2=??? ref=C:\bbmap\resources\truseq.fa.gz ktrim=r k=???? mink=???? hdist=????

??? For out1 and out2 do I need to create some kind of new file?
??? I don't know what to put for k, mink and hdist, should k be 33 because the adapter sequences are 33 bases? not sure about mink and hdist.

Thank you. Merry Christmas
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