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AIRR Community Data Standards
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Update '10X Chromium' to include other single cell technologies #810

Open ustervbo opened 1 week ago

ustervbo commented 1 week ago

Currently, the subsection 10X Chromium is focused on 10x, but other manufacturers have entered the single cell arena. Methods like TIRTL-seq may also gain traction.

We should update the section to be more platform independent.

bcorrie commented 1 week ago

Yes, this should probably be generalized towards describing single-cell experiments maybe using 10X as an example.

I see that TIRTL-seq uses MiXCR (at least in the paper) does anyone know if their AIRR support includes cell_index for paired chains? I see that MiXCR has an exportAIRR command, but it isn't on the list of "AIRR compliant software" so hasn't passed the certification. We have never used MiXCR to process a study with paired chains, so not sure if a paired chain study in the AIRR format would properly represent paired chains???

Of course 10X is not on the supported software list either, but I know their output is AIRR compliant as we load their data, so this is mostly out of curiosity more than anything else.

scharch commented 1 week ago

Like 10X, it's closed source (AFAIK). But the exportAIRR works well enough. Dunno about paired chains.

ustervbo commented 1 week ago

TIRTL-seq identified likely combinations of TCRa and b using 384 well plates with about 25000 cells/well. The indices you have in TIRTL-seq are for the wells, not the cells.

Other approaches connect TCRa-b and BCR H-L at the single cell level. There are no identifying indices apart from (maybe) UMIs.

On Mon, 28 Oct 2024 at 18:58, Chaim Schramm @.***> wrote:

Like 10X, it's closed source (AFAIK). But the exportAIRR works well enough. Dunno about paired chains.

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