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nf-core / scrnaseq

A single-cell RNAseq pipeline for 10X genomics data
https://nf-co.re/scrnaseq
MIT License
179 stars 155 forks source link

Add RNA Velocity #14

Open olgabot opened 4 years ago

olgabot commented 4 years ago

Tutorial: https://www.kallistobus.tools/velocity_tutorial.html

The sticking point is getting introns programmatically from every possible GTF. I've had success with gffutils.FeatureDB.create_introns before but haven't implemented it yet

ftucos commented 3 years ago

Probably would be easier to use STAR to generate the RNA velocity matrix just by adding this option --soloFeatures Gene Velocyto

grst commented 2 years ago

Alevin also supports RNA velocity: https://combine-lab.github.io/alevin-tutorial/2020/alevin-velocity/

Would be nice to support it for all three methods eventually.

Vivian-chen16 commented 1 year ago

In that case, are we going to set --solofeature as another option(i.e. parse in from input channel) for star? @ftucos @grst There's another PR regarding to genomic feature. We can have it as dropdown menu also to match with user's preference

grst commented 1 year ago

The interface I would have envisaged (happy to discuss) is to set a global parameter, e.g. --with_velocity and the appropriate parameters are added depending on whether salmon/kallisto/starsolo are chosen as aligner.

AFAIK cellranger doesn't support RNA velocity natively, but an additional process using velocyto.py could be added. It is incredibly slow though in my experience.

Vivian-chen16 commented 1 year ago

Addressed in PR https://github.com/nf-core/scrnaseq/pull/168

apeltzer commented 1 year ago

Only closing when we have support for it in all cases - STAR is a good one, but kallisto bustools missing, alevin is also not there I think so far