Usage on bulk RNA-seq samples

[Grigory Nos]

Dear Immcantation developers team!

Thanks a lot for this amazing software

I want to ask if Immcantation and Presto, in particular, can work with a common bulk RNA-seq library without any target enrichment of vdj genes?

If not, do you have any plans to make it?

Thanks a lot

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[Jason Vander Heiden]

Thanks @{5e674baa7075ba0cf83e0b22} !

No, it doesn’t work on bulk RNA-seq data and I don’t think there are any plans to add that functionality. If the bulk RNA-seq doesn’t require contig assembly (eg, 2x150 reads), then something could be cobbled together with presto. But, in that case I would still probably try MiXCR’s implementation first: https://mixcr.readthedocs.io/en/master/rnaseq.html

The next MiXCR release (v3.0.14) should have support for the AIRR Rearrangement standard, which will simplify plugging the output into the various immcantation tools.

[ssnn]

This seems to be resolved. Reopen if needed.