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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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Using for cite-seq #257

Closed curtisd0886 closed 3 years ago

curtisd0886 commented 3 years ago

Would it be possible to use zUMIs to find feature barcodes in CITE-seq? My though was to make a STAR index file with the CITE-seq sequences and then map with zUMIs. When I have tried this I get an error because all the reads end up in the unmapped bam file. Is there a way to make this work? I think the issue may be with generating an index file with a fasta that contains many small (15nt) sequences.

cziegenhain commented 3 years ago

I don't think you can map 15 bp efficiently as a "cDNA" but it would depend on the number of sequences and the settings within star. Sorry to say we don't currently have a solution for cite-seq, maybe in the future. Best, Christoph