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immcantation / presto

pRESTO is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq). pRESTO is a bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
https://presto.readthedocs.io
GNU Affero General Public License v3.0
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Usage on bulk RNA-seq samples #78

Closed ssnn-airr closed 3 years ago

ssnn-airr commented 3 years ago

Original report by Grigory Nos (Bitbucket: [Grigory Nos](https://bitbucket.org/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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ssnn-airr commented 3 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

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-airr commented 3 years ago

This seems to be resolved. Reopen if needed.