removing last two runs from RunInfo.xml for bcl2fastq
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1
Entering edit mode
6.6 years ago
alex ▴ 230

Hi all,

We are currentlying using bcltofastq 2.1.5 on our nextseq.  

Running:

bcl2fastq --runfolder-dir ~/run/ --output-dir ~/out/ --interop-dir ~/run/InterOp/

and we have in our runInfo

<Reads>

<Read Number="1" NumCycles="100" IsIndexedRead=“N" />

<Read Number="2" NumCycles="8" IsIndexedRead=“Y" />

<Read Number="3" NumCycles="8" IsIndexedRead=“N" />

<Read Number="4" NumCycles="100" IsIndexedRead=“N" />

</Reads>

is there a good way to delete or comment or ignore Read Numbers 3 and 4 from the command line?  Thanks

 

bcl illumina • 2.3k views
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2
Entering edit mode
5.8 years ago
Paul ★ 1.4k

Dear Alex,

you do not need to delete those lines. You can just use parameter:

--use-bases-mask y100,i8,i8,y100

Paul.

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