Hi!
Thanks for developing Tracer!
I am using it with a dataset of ~4k cells and there is something strange with the output of assemble with one specific cell. The file filtered_TCRs.txt outputs two Beta chains but both have the same ID (see below). When you look closely you can note the following:
Both chains share the CDR3 sequence, the D and the J segment.
The V segment only differs in the allele of the usage (TRBV7-8*01 vs. TRBV7-8*03)
The TPM of the first cell is unusually small (3.29) while the second one has values similar to other detected chains in my dataset (1472)
In both chains the TRBV7-8*01 has 100 % identity, while TRBV7-8*03 has 99.286 and 99.303, respectively. However *03 allele was chosen in the first chain.
I don't know if this is unexpected behaviour. Should I assume both chains are the same? or is there a significant difference between the two sequences?
The output of unfiltered_TCR.txt is exactly the same as filtered_TCR.txt.
#TCR_B#
##TRINITY_DN0_c0_g1_i2##
V segment: TRBV7-8*03
D segment: TRBD1*01
J segment: TRBJ2-2*01
ID: TRBV7-8_AGACGCTCAGGGGTGGTCACCG_TRBJ2-2
TPM: 3.29375
Productive: True
Stop codon: False
In frame: True
CDR3aa: ASRRSGVVTGELF
CDR3nt: GCCAGCAGACGCTCAGGGGTGGTCACCGGGGAGCTGTTT
Segment query_id subject_id % identity alignment length mismatches gap opens gaps
q start q end s start s end e value bit score
V reversed|TRINITY_DN0_c0_g1_i2 TRBV7-8*03 99.286 140 1 0 0 78 217 148
287 2.40e-58 216
V reversed|TRINITY_DN0_c0_g1_i2 TRBV7-8*01 100.000 137 0 0 0 78 214 148
284 7.08e-58 215
V reversed|TRINITY_DN0_c0_g1_i2 TRBV7-8*02 99.270 137 1 0 0 78 214 148
284 6.14e-57 212
V reversed|TRINITY_DN0_c0_g1_i2 TRBV7-4*01 89.362 141 15 0 0 74 214 144
284 1.11e-45 174
V reversed|TRINITY_DN0_c0_g1_i2 TRBV7-2*01 93.496 123 8 0 0 92 214 162
284 8.34e-44 168
D reversed|TRINITY_DN0_c0_g1_i2 TRBD1*01 100.000 6 0 0 0 220 225 5
10 4.0 12.4
J reversed|TRINITY_DN0_c0_g1_i2 TRBJ2-2*01 100.000 47 0 0 0 230 276 5
51 1.93e-22 93.7
##TRINITY_DN0_c0_g1_i1##
V segment: TRBV7-8*01
D segment: TRBD1*01
J segment: TRBJ2-2*01
ID: TRBV7-8_AGCAGACGCTCAGGGGTGGTCACCG_TRBJ2-2
TPM: 1472.31
Productive: True
Stop codon: False
In frame: True
CDR3aa: ASRRSGVVTGELF
CDR3nt: GCCAGCAGACGCTCAGGGGTGGTCACCGGGGAGCTGTTT
Segment query_id subject_id % identity alignment length mismatches gap opens gaps
q start q end s start s end e value bit score
V reversed|TRINITY_DN0_c0_g1_i1 TRBV7-8*01 100.000 284 0 0 0 16 299 1
284 8.99e-127 444
V reversed|TRINITY_DN0_c0_g1_i1 TRBV7-8*03 99.303 287 2 0 0 16 302 1
287 2.65e-126 442
V reversed|TRINITY_DN0_c0_g1_i1 TRBV7-8*02 99.648 284 1 0 0 16 299 1
284 7.80e-126 441
V reversed|TRINITY_DN0_c0_g1_i1 TRBV7-6*01 90.845 284 26 0 0 16 299 1
284 2.21e-102 363
V reversed|TRINITY_DN0_c0_g1_i1 TRBV7-4*01 90.493 284 27 0 0 16 299 1
284 1.91e-101 360
D reversed|TRINITY_DN0_c0_g1_i1 TRBD1*01 100.000 6 0 0 0 305 310 5
10 4.5 12.4
J reversed|TRINITY_DN0_c0_g1_i1 TRBJ2-2*01 100.000 47 0 0 0 315 361 5
51 2.17e-22 93.7
Hi! Thanks for developing Tracer! I am using it with a dataset of ~4k cells and there is something strange with the output of assemble with one specific cell. The file
filtered_TCRs.txt
outputs two Beta chains but both have the same ID (see below). When you look closely you can note the following:I don't know if this is unexpected behaviour. Should I assume both chains are the same? or is there a significant difference between the two sequences? The output of
unfiltered_TCR.txt
is exactly the same asfiltered_TCR.txt
.