removing last two runs from RunInfo.xml for bcl2fastq

Question

[alex]

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

Answer 1

[Paul]

Dear Alex,

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

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

Paul.