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sumeetg23/I5OnlyDemultiplex-I7AsRead

Created June 29, 2021 13:55
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How to demultiplex based on I5 index and have I7 index as a separate read
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I5OnlyDemultiplex-I7AsRead
If you want the I7 indexes on a standalone FastQ file (R2 file will have the I7 indexes), then
Step 1. first modify your RunInfo.xml file by changing
<Read Number="2" NumCycles="8" IsIndexedRead="Y" />
to
<Read Number="2" NumCycles="8" IsIndexedRead="N" />.
Step 2. Now, run bcl2fastq with the following options: --use-bases-mask y*,y*,i*,y* --minimum-trimmed-read-length 0 --mask-short-adapter-reads 0
Command (software will only use i5 for demultiplexing):
bcl2fastq --runfolder-dir=<run folder> --output-dir=<run folder> --sample-sheet=<samplesheet in csv format> --use-bases-mask y*,y*,i*,y* --minimum-trimmed-read-length 0 --mask-short-adapter-reads 0
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