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velocyto-team / velocyto.R

RNA velocity estimation in R
http://velocyto.org
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RUN 10X on cellranger aggr library? #63

Open x811zou opened 5 years ago

x811zou commented 5 years ago

Hi! I ran cellranger aggr to generated a pooled bam file from several 10X scRNA-seq data (different time points data). But velocyto could generate loom file from this pooled bam file with the reference. Is there a way to solve this? Or do I have to run velocyto for each bam file separately?

pkharchenko commented 5 years ago

Hi Zou, Not sure I understand the technical problem you’re encountering. But for the purposes of velocyto, you can read in three loom files and them simply combine the spliced / unspliced matrices from the tree different experiments. That said, if there’s a notable batch effect between the experiments, that could skew the results. Best, -peter.

On Jan 28, 2019, at 11:52 AM, Xue Zou notifications@github.com wrote:

Hi! I ran cellranger aggr to generated a pooled bam file from several 10X scRNA-seq data (different time points data). But velocyto could generate loom file from this pooled bam file with the reference. Is there a way to solve this? Or do I have to run velocyto for each bam file separately?

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x811zou commented 5 years ago

If I combine them, would I be able to label them based on the sample name?

pkharchenko commented 5 years ago

I would tack on sample name onto the name of each cell.

On Jan 29, 2019, at 8:59 AM, Xue Zou notifications@github.com wrote:

If I combine them, would I be able to label them based on the sample name?

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