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velocyto-team / velocyto.py

RNA velocity estimation in Python
http://velocyto.org/velocyto.py/
BSD 2-Clause "Simplified" License
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ERROR - Can not locate the barcodes.tsv file! for Cellranger Multiplexing outputs #323

Open danli349 opened 2 years ago

danli349 commented 2 years ago

The Cellranger Multiplexing outputs has a different folder direction: image The command

velocyto run10x -m mm10_rmsk.gtf TCEVdox015-12677-1 gtf/Mus_musculus.GRCm38.93_costom_filtered3.gtf

has an error 

ERROR - Can not locate the barcodes.tsv file!

Can someone tell me how to run the velocyto run10x command for Multiplexing outputs? Thanks

danli349 commented 2 years ago

There is only raw_feature_bc_matrix, no filtered_feature_bc_matrix folder, nor the analysis folder in Multiplexing output.

danli349 commented 2 years ago

There is only unassigned_alignments.bam, no possorted_genome_bam.bam in folder of Multiplexing output.

bsmith030465 commented 2 years ago

danli,

Were you able to find a solution to using velocyto with cellranger multi (i.e. multiplexing) outputs?

thanks!!

MugenQin commented 1 year ago

Did someone solve this problem or run the rule cellranger pipeline again？

danli349 commented 1 year ago

@bsmith030465 @MugenQin I run cellranger multi first to get the cell barcode assignment, then run cellranger count without demultiplex, and then velocyto run10x using the cellranger count output. Then use the cell barcode assignment to analyze the velocyto output.