How can I get mapping rate for each cell?

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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How can I get mapping rate for each cell? #303

Closed diyang1354 closed 2 years ago

diyang1354 commented 2 years ago

Hi, In the running log, I can see the alignment rate in the output of Rsubread. Is this alignment rate calculated with respect to all the reads in the fastq file? How can I get the alignment rate for each individual barcode? Thanks.

cziegenhain commented 2 years ago

Hi,

You can find this information as a text file and an automatically generated plot in the zUMIs_output/stats folder.

Best, Christoph