What is the difference between `possorted_genome_bam.bam` in the output of `cellranger count` and `sample_alignments.bam` in the output of `cellranger multi`?

Question

[Dan]

Hello:

I am trying to run single-cell RNA-seq velocity analysis by velocyto run10x (https://velocyto.org/velocyto.py/tutorial/cli.html) using the output of cellranger multi with hashtag multiplex. Could someone please let me know what the difference between "possorted_genome_bam.bam" in the output of cellranger count with no multiplex, and sample_alignments.bam in the output of cellranger multi with multiplex? Can I use the sample_alignments.bam in the output of cellranger multi to run velocyto run10x?

Thanks a lot.