lakigigar
commented
8 years ago Hi Valentine,
Thanks! We are thinking about demultiplexing but have not tackled that step for now. We do have a workflow for 10x that starts after the demultiplexing that we've just posted and that you might find useful for some of the technologies you mentioned as well (we plan mods for some of them in the near future). See
https://pachterlab.github.io/kallisto/singlecell.html
You are right that many of the steps (including demultiplexing) might be best handled internally in kallisto and we're looking at that. Lior
On Fri, Jun 3, 2016 at 4:05 AM, Valentine Svensson <notifications@github.com
wrote:
Hi,
I am very excited that there finally is a tool out that does proper UMI quantification! I will retire my heuristic method https://github.com/vals/umis and recommend this in it's place.
There are a couple of use cases though which might be problematic from a practical stand point.
Firstly, this requires the cells to be demultiplexed from each other. In many protocols, e.g. CEL-seq or MARS-seq, the cellular barcode is not demultiplexed by the Illumina pre-processing pipeline. Do you have any recommendations for demultiplexing?
Additionally, in the more recent nanoliter droplet based protocols, there are hundreds of thousands of potential cellular barcodes. Usually an experiment only captures a few thousand cells, but demultiplexing in to files before seeing which ones actually contained cells does not work well with most file systems. In my heuristic script, I handled this by doing cellular barcode demultiplexing internally and returning a table. Is there any way Kallisto could do the demultiplexing internally, similar to how UMI's are handled?
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jbergenstrahle
hmassalha
Hi,
I am very excited that there finally is a tool out that does proper UMI quantification! I will retire my heuristic method and recommend this in it's place.
There are a couple of use cases though which might be problematic from a practical stand point.
Firstly, this requires the cells to be demultiplexed from each other. In many protocols, e.g. CEL-seq or MARS-seq, the cellular barcode is not demultiplexed by the Illumina pre-processing pipeline. Do you have any recommendations for demultiplexing?
Additionally, in the more recent nanoliter droplet based protocols, there are hundreds of thousands of potential cellular barcodes. Usually an experiment only captures a few thousand cells, but demultiplexing in to files before seeing which ones actually contained cells does not work well with most file systems. In my heuristic script, I handled this by doing cellular barcode demultiplexing internally and returning a table. Is there any way Kallisto could do the demultiplexing internally, similar to how UMI's are handled?