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Old 09-23-2014, 03:01 AM   #5
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Join Date: Jun 2009
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Originally Posted by cnicolet View Post
this is a little off topic from the thread but seems related to some of the things both you guys are doing--do you have a slick way to zcat the bcl2fastq output correctly? I've been doing it "by hand" two files at a time
I'm using a modified version of a script from Shingo Kikugawa
It's single thread, so takes a while. It's still quicker than manual zcatting.

I spoke to Illumina about this and a version of bcl2fastq is in the pipeline that will have a flag to stop lane splitting of fastq.
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