dstcr
commented
1 year ago Dear Dekosky Lab, Great paper! I was interested in your technology and downloaded data from PRJNA827461 to have a look myself. After parsing through my own pipeline, I found that the 'TCR_presort_sequences' amounted to around 60,000 clonotypes and wondered if this was the entire repertoire from Donor 1?
Furthermore, when looking at the paired clonotypes there seems to be many clones where the same beta chain is paired with many alpha chains, which we wouldn't expect to see in a typical repertoire (max 2 given dual alpha chains).
I have attached the clonotype table I produced from the data. Is this something you usually see in the data, and do you have a fidelity metric that you apply to the data? Many thanks
All these pairs have the same specificity? It would suggest wide-spread reoccurance of the same beta chains in separate clonotypes.
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TRAV13-2 | TRBV7-9 | TRAJ50 | TRBJ2-1 | CASTYPEGYNEQFF | CAASETSYDKVIF | 9010 -- | -- | -- | -- | -- | -- | -- TRAV26-1 | TRBV7-9 | TRAJ24 | TRBJ2-1 | CASTYPEGYNEQFF | CIVRVGGDSWGKLQF | 4556 TRAV13-2 | TRBV7-9 | TRAJ50 | TRBJ2-1 | CASTYPEGYNEQFF | CAEMETSYDKVTF | 1285 TRAV13-1 | TRBV7-9 | TRAJ50 | TRBJ2-1 | CASTYPEGYNEQFF | CAASETSYDKVIF | 958 TRAV13-1 | TRBV7-9 | TRAJ39 | TRBJ2-1 | CASTYPEGYNEQFF | CAASVDAGNMLTF | 599 TRAV2 | TRBV7-9 | TRAJ35 | TRBJ2-1 | CASTYPEGYNEQFF | CAVEDKGFGNVLHC | 141 TRAV2 | TRBV7-9 | TRAJ20 | TRBJ2-1 | CASTYPEGYNEQFF | CAVNNDYKLSF | 104 TRAV21 | TRBV7-9 | TRAJ6 | TRBJ2-1 | CASTYPEGYNEQFF | CAVTSGGSYIPTF | 98 TRAV2 | TRBV7-9 | TRAJ26 | TRBJ2-1 | CASTYPEGYNEQFF | CAVDNYGQNFVF | 84 TRAV26-1 | TRBV7-9 | TRAJ30 | TRBJ2-1 | CASTYPEGYNEQFF | CIVREGNRDDKIIF | 73 TRAV2 | TRBV7-9 | TRAJ20 | TRBJ2-1 | CASTYPEGYNEQFF | CAVNDYRLSF | 61 TRAV2 | TRBV7-9 | TRAJ8 | TRBJ2-1 | CASTYPEGYNEQFF | CAVEELNTGFQKLVF | 58 TRAV13-2 | TRBV4-1 | TRAJ50 | TRBJ2-1 | CASTYPEGYNEQFF | CAASETSYDKVIF | 51 TRAV21 | TRBV7-9 | TRAJ23 | TRBJ2-1 | CASTYPEGYNEQFF | CAVMGNQGGKLIF | 45 TRAV26-2 | TRBV7-9 | TRAJ10 | TRBJ2-1 | CASTYPEGYNEQFF | CIVITGGGNKLTF | 41 TRAV26-2 | TRBV7-9 | TRAJ36 | TRBJ2-1 | CASTYPEGYNEQFF | CILQTGANNLFF | 40 TRAV12-2 | TRBV7-9 | TRAJ23 | TRBJ2-1 | CASTYPEGYNEQFF | CAVNSFYNQGGKLIF | 36 TRAV12-2 | TRBV7-9 | TRAJ20 | TRBJ2-1 | CASTYPEGYNEQFF | CAVNNDYKLSF | 24 TRAV13-1 | TRBV7-9 | TRAJ9 | TRBJ2-1 | CASTYPEGYNEQFF | CAASEGGFKTIF | 23 TRAV12-2 | TRBV7-9 | TRAJ43 | TRBJ2-1 | CASTYPEGYNEQFF | CAVNFPPDMRF | 19 TRAV35 | TRBV7-9 | TRAJ43 | TRBJ2-1 | CASTYPEGYNEQFF | CAGCFNDMRF | 18 TRAV21 | TRBV7-9 | TRAJ57 | TRBJ2-1 | CASTYPEGYNEQFF | CAVTQGGSEKLVF | 16 TRAV13-2 | TRBV7-9 | TRAJ50 | TRBJ2-1 | CASTYPEGYNEQFF | CAEMENSYDKVIC | 14 TRAV13-2 | TRBV7-9 | TRAJ50 | TRBJ2-1 | CASTYPEGYNEQFF | CAEMETSYDKGIV | 13 TRAV2 | TRBV11-2 | TRAJ26 | TRBJ2-1 | CASTYPEGYNEQFF | CAVDNYGQNFVF | 13 TRAV13-2 | TRBV7-3 | TRAJ50 | TRBJ2-1 | CASTYPEGYNEQFF | CAASETSYDKVIF | 11 TRAV13-2 | TRBV7-9 | TRAJ50 | TRBJ2-1 | CASTYPEGYNEQFF | CAAGETSYAKVIF | 10 TRAV13-2 | TRBV7-9 | TRAJ50 | TRBJ2-1 | CASTYPEGYNEQFF | CAEMETTYGKVIF | 7 TRAV13-2 | TRBV7-4 | TRAJ50 | TRBJ2-1 | CASTYPEGYNEQFF | CAASETSYDKVIF | 6 TRAV13-2 | TRBV7-9 | TRAJ50 | TRBJ2-1 | CASTYPEGYNEQFF | CAEMEASYDGVIF | 5 TRAV13-2 | TRBV7-9 | TRAJ50 | TRBJ2-1 | CASTYPEGYNEQFF | CAEMETSYDNVIL | 5 TRAV13-1 | TRBV7-9 | TRAJ22 | TRBJ2-1 | CASTYPEGYNEQFF | CAASDGSARQLTF | 4 TRAV13-2 | TRBV7-9 | TRAJ50 | TRBJ2-1 | CASTYPEGYNEQFF | CAEIETSYDKVIL | 4 TRAV13-2 | TRBV7-9 | TRAJ50 | TRBJ2-1 | CASTYPEGYNEQFF | CAEMGTSYEKVIF | 4 TRAV13-2 | TRBV7-9 | TRAJ50 | TRBJ2-1 | CASTYPEGYNEQFF | SAEMETSYDKVIC | 4 TRAV13-1 | TRBV7-9 | TRAJ50 | TRBJ2-1 | CASTYPEGYNEQFF | CAAGETSYAKVIF | 3 TRAV13-1 | TRBV7-9 | TRAJ50 | TRBJ2-7 | CASTYPEGYNEQFF | CAASETSYDKVIF | 3 TRAV13-2 | TRBV27 | TRAJ50 | TRBJ2-1 | CASTYPEGYNEQFF | CAASETSYDKVIF | 3 TRAV13-2 | TRBV4-1 | TRAJ50 | TRBJ2-1 | CASTYPEGYNEQFF | CAEMETSYDKVTF | 3 TRAV13-2 | TRBV7-9 | TRAJ50 | TRBJ2-1 | CASTYPEGYNEQFF | CEGMETSYDKVTC | 3
Dear Dekosky Lab, Great paper! I was interested in your technology and downloaded data from PRJNA827461 to have a look myself. After parsing through my own pipeline, I found that the 'TCR_presort_sequences' amounted to around 60,000 clonotypes and wondered if this was the entire repertoire from Donor 1?
Furthermore, when looking at the paired clonotypes there seems to be many clones where the same beta chain is paired with many alpha chains, which we wouldn't expect to see in a typical repertoire (max 2 given dual alpha chains).
I have attached the clonotype table I produced from the data. Is this something you usually see in the data, and do you have a fidelity metric that you apply to the data? Many thanks
SRR19119688_clonotypes.xlsx