Yuanjian Huang

Same issue here. Any suggestions?

`velocyto run10x` requires the Cell Ranger outputs like below  use codes like below ```python velocyto run10x -@ 16 -m /mnt/d/KP/hg38_rmsk.gtf /home/hyjforesight/SMC05T/ /mnt/d/KP/refdata-gex-GRCh38-2020-A-modified/genes/genes.gtf ```

hello @Sa753 we also did multiplexed scRNA-seq. As I remember, velocyto run10x didn't work for cell ranger multi. you should use velocyto (on any technique) for individual bam 

hello @Sa753 if your samples were prepared by 10X cell plex kit, you will get 2 libraries after sequencing. One is oligo, the other is sequencing data (Sorry, I don't...

hello @Sa753 try this ```linux # sort individual bam first samtools sort /home/hyjforesight/sorting/Apc_Tumor.bam -o /home/hyjforesight/sorting/possorted_Apc_Tumor.bam -@ 16 # use the 10X barcodes.tsv and 10X reference genome file velocyto run -@...

Hello @Sa753 Please use the assigned.bam. As I remember, I renamed this bam into the format of possorted_XXX.bam, so that velocyto doesn't resort it again. And unzip the barcodes file...

genes.gtf is broken. try to tar refdata-cellranger-GRCh38-3.0.0.tar.gz again.

@GouQiao see here https://github.com/velocyto-team/velocyto.py/issues/250

Can not locate the barcodes.tsv file---- u need the barcodes.tsv change all the files into an absolute path

I checked the chromosome name in bam file. It's chrM, not chrMT. So, what @kpy619 said is not right, which means velocy.py didnt map the mito genes in bam to...