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COMBINE-lab / salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
https://combine-lab.github.io/salmon
GNU General Public License v3.0
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Possible to add support for 10x VDJ? #861

Open jeremymsimon opened 1 year ago

jeremymsimon commented 1 year ago

The answer here could simply be 'no' 😄 but as this question came up recently for me, and it is one I've seen mentioned on the nf-core/scrna slack, I figured I'd raise it here to get your thoughts.

There is a standard CellRanger workflow for the 10x V(D)J approach (https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/using/vdj)

Is this something remotely achievable with alevin/alevin-fry? It would be great for those who have matched 10x scRNA-seq to be able to process everything with the same package!

rob-p commented 1 year ago

Hi @jeremymsimon,

I think this is something that we do want to support. Are you familiar with the protocol and what types of changes / additions might need to be made in order to support processing this type of data?

--Rob

jeremymsimon commented 1 year ago

Hey @rob-p , I know virtually nothing about this, but I've been having somewhat related discussions lately with @mourisl about their method TRUST4 (https://github.com/liulab-dfci/TRUST4)

Li seemingly has interest in helping out with this, and coincidentally is the developer of chromap too in case support for ATACseq is also coming soon!

I'll let you both take it from here and looking forward to testing!