Documentation for output columns generated by the 10x-sc-xcr-vdj preset

[BIGM0RPH]

Hi,

I'm using the 10x-sc-xcr-vdj preset and was wondering if there is any documentation that explains the meaning of each column in the output generated by this pipeline.

Specifically, I'm looking for documentation describing the following headers:

cellGroup
groupReadCount
groupUniqueCellCount
groupUniqueMoleculeCount
TRA.cloneCount
TRB.cloneCount
TRA.primary.readCount
TRA.second.readCount
TRB.primary.readCount
TRB.second.readCount
TRA.primary.uniqueMoleculeCount
TRA.second.uniqueMoleculeCount
TRB.primary.uniqueMoleculeCount
TRB.second.uniqueMoleculeCount
TRA.primary.bestVHit
TRA.second.bestVHit
TRB.primary.bestVHit
TRB.second.bestVHit
TRA.primary.bestDHit
TRA.second.bestDHit
TRB.primary.bestDHit
TRB.second.bestDHit
TRA.primary.bestJHit
TRA.second.bestJHit
TRB.primary.bestJHit
TRB.second.bestJHit
TRA.primary.bestCHit
TRA.second.bestCHit
TRB.primary.bestCHit
TRB.second.bestCHit
TRA.primary.nSeqCDR3
TRA.second.nSeqCDR3
TRB.primary.nSeqCDR3
TRB.second.nSeqCDR3
TRA.primary.aaSeqCDR3
TRA.second.aaSeqCDR3
TRB.primary.aaSeqCDR3
TRB.second.aaSeqCDR3

I have searched through the documentation but haven't been able to find a page describing these fields or explaining concepts such as the primary vs second chains and the various read/molecule count columns.

Is there a reference page, schema, or documentation that explains each of these output columns? If not, could you briefly explain what these fields represent or point me to the relevant source?

Thank you!

[mizraelson]

Hi,
For single cell data MiXCR allows two chains to be assembled: primary (the most abundant) and secondary (less abundant).
For each chain you get the full info: V, (D) , J genes as well as the amino-acid and nucleotide sequences.
MiXCR also assmebles cells into groups with similar chains. For example if you have 500 cells with TCRA chain "a" and TCRB chain "b", there will be a cell group of 50 cells.

cellGroup - is the id of this group
groupReadCount - total number of reads in that group
groupUniqueCellCount - number of cells in this group
groupUniqueMoleculeCount - number of UMIs
TRA.cloneCount - number of TRA clones (primary and secondary or just primary)
TRA.primary.readCount - number of reads for this specific clone in this cell
TRA.primary.uniqueMoleculeCount - number of UMIs for this specific clone in this cell