Read data from TraCeR ([SLonnbergP+16]).
Requires the TraCeR output directory which contains a folder for each cell. Unfortunately the results files generated by
tracer summarizedo not contain all required information.
The function will read TCR information from the
- Reading data into Scirpy has the following constraints:
Each cell can have up to four productive chains chains (Dual IR): two VJ and two VDJ chains.
Excess chains are ignored (those with lowest read count/UMI count) and cells flagged as Multichain-cell.
Non-productive chains are ignored.
Chain loci must be valid IMGT locus names.
Excess chains, non-productive chains, chains without a CDR3 sequence, or chains with invalid loci are serialized to JSON and stored in the
extra_chainscolumn. They are not used by scirpy except when exporting the
AnnDataobject to AIRR format.
For more information, see Immune receptor (IR) model.