unassigned clone id

[saramoein372]

Description of the question

Hi Kelvin,

I have some questions about the clone_id after running the dandelion:

1- in the vdj.metadata there is column clone_id. Also, in vdj.data there in a clone_id. The problem I have is that for some of the cells, the vdj.metadata has clone_id, but for the same cells, the vdj.data does not have any clone_is. Why is that?

2- Why some of the cells have no clone_id?
3- How is it possible that many cells with "unassigned" clone_id" make a clone?

Thanks,
Sara

Minimal example

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Any error message produced by the code above

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OS information

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Version information

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Additional context

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[zktuong]

1- in the vdj.metadata there is column clone_id. Also, in vdj.data there in a clone_id. The problem I have is that for some of the cells, the vdj.metadata has clone_id, but for the same cells, the vdj.data does not have any clone_is. Why is that?

I suspect some cells have multiple contigs and only a subset of them are used. The data structure in the latest version should make this very clear - is this still the same if you re-initialise the data with the latest version?

vdj = ddl.read_h5('file.h5') # assuming file.h5 is a files saved from a previous version of dandelion
ddl.update_metdata(vdj, reinitialize = True)

2- Why some of the cells have no clone_id?

because these cells don't have heavy chains.

3- How is it possible that many cells with "unassigned" clone_id" make a clone?

This is a bug that should be fixed in the latest version. please try reinstall and updating the metadata as above.