Does ALICE work on paired alpha-beta data?

pogorely / ALICE

Detecting TCR involved in immune responses from single RepSeq datasets

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Does ALICE work on paired alpha-beta data? #12

Open hejing3283 opened 4 years ago

hejing3283 commented 4 years ago

I am having paired alpha-beta data. Does ALICE also works on paired alpha-beta data?

pogorely commented 4 years ago

Hi,

The current version works on single-chain data. In general, ALICE works better on large (and thus bulk) RepSeq datasets. However, if your dataset is sufficiently large (=at least thousands of unique clonotypes), you could try to use ALICE on a single chain (TRB) from your dataset to identify interesting clones.

dstcr commented 2 years ago

Is it still limited to single chain data?