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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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aligning to multiple genomes? #387

Closed brennaremick closed 8 months ago

brennaremick commented 8 months ago

I would like to align my reads to 2 genomes (human genome and a viral genome). Is this possible with zUMIs?

cziegenhain commented 8 months ago

Hi, should not be a problem. You can either make a STAR reference genome with all the fasta files that you want to map against or you can add smaller fasta files (eg. viral genome) to a regular run against the human genome on the fly in zUMIs. Simply input the fasta in the YAML section reference: additional_files: , see line 34 here https://github.com/sdparekh/zUMIs/blob/main/zUMIs.yaml#L34