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Teichlab / tracer

TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
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problem understanding tracer output #85

Closed hkoohy closed 5 years ago

mstubb commented 5 years ago

Hi Hashem,

This issue is currently empty! Happy to help if you can add a bit more context :)

Mike

hkoohy commented 5 years ago

Hi Mike, Sorry to bother you again for another question: In our tracer output (cell data file where we see clone groups and sizes), for some cells we both productive A and B chain, but the clonal_group and 'group_size' is left blanked! Does this mean that the chains are unpaired? please see the following for an example: many thanks

cell_name A_productive A_unproductive B_productive B_unproductive clonal_group group_size P01-PP10A2-T3-S1-Sc_S98_L00_al TRAV12-2_CCGTGGGTGGGA_TRAJ7 1 59 P01-PP10A4-T4-S2-Sc_S100_L00_a TRAV12-2_GTGAAGGGAGGAAA_TRAJ47 TRBV4-1_GCCAATGGGGACAAGATA_TRBJ2-3 4 14 P01-PP10A5-T4-S2-Sc_S101_L00_a TRAV12-2_TGAACGGAGACAAC_TRAJ21 TRBV2_AGCAGCCCCCCGGGGGAGCA_TRBJ2-7
P01-PP10A6-T4-S2-Sc_S102_L00_a TRAV12-2_GCCGTATCAGG_TRAJ45 TRBV4-1_CAGCCGTGCGGTCAGCGATAC_TRBJ2-3 13 5

hkoohy commented 5 years ago

It looks that these are singletons! right?

mstubb commented 5 years ago

Yes, exactly. If these entries are blank then that cell doesn't have any apparent clonal relationships and is a singleton.

hkoohy commented 5 years ago

thanks