Demultiplexing Only Part Of A Pe Flowcell With Casava 1.8.2
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10.6 years ago
Dan D 7.3k

We have an Illumina HiSeq2000 paired-end 100 run that had a clog, so the data for all lanes are junk after ~cycle 160. We would like to demultiplex the good data we have, but I've never demultiplexed a partial flowcell and the user's guide doesn't go into detail about how to perform such an operation. Has anyone done this before?

illumina next-gen • 1.8k views
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were the barcodes sequenced properly?

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Yes, the data were beautiful until the clog. Thanks, and good question!

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10.6 years ago
Dan D 7.3k

Nevermind, I answered my own question. It wasn't clear at first, but the --use-bases-mask parameter is the key! It's discussed on page 33 of the CASAVA 1.8.2 user guide.