ERROR - Can not locate the barcodes.tsv file! for Cellranger Multiplexing outputs

[danli349]

The Cellranger Multiplexing outputs has a different folder direction: 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]

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

[danli349]

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

[bsmith030465]

danli,

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

thanks!!