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Demultiplexing Only Part Of A Pe Flowcell With Casava 1.8.2

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
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written by Dan D Dan D

were the barcodes sequenced properly?

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written by Istvan Albert Istvan Albert

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

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written by Dan D Dan D

1 answer

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.

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written by Dan D Dan D

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