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sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
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BD Rhapsody compatability #271

Closed alanaleah89 closed 3 years ago

alanaleah89 commented 3 years ago

Is there a way to insert 3 separate whitelist files?
The BD Rapsody single cell analysis system contains 3 BCs. Can zUMIs accept this type of parameter and if so should this file path be separated by a comma or a space?

cziegenhain commented 3 years ago

Hi,

zUMIs will paste the three bits of barcode into one unique string when extracting from your fastq reads, so in your whitelist you should give the expected combinations in a single file. You can use expand.grid() in R to find the unique combinations easily.

There is no option inbuilt for several whitelists.

Best, C

cziegenhain commented 3 years ago

Feel free to reopen if you need further input.