TCRViz uses a fasta like file format:
- For each TR[A/B]V gene (see ) one fasta entry is generated in each .viz file (nucleotide, unique nucleotide and protein .viz file).
- The header of each fasta entry contains the TR[A/B]V gene name.
- The body of each fasta entry contains the information of CDR3 length and the TR[A/B]J genes rearranged with the TR[A/B]V gene denoted in the header.
- Example entry :
> TRBV 11-2*03
9 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 1
11 17 4 0 1 0 0 0 0 0 0 0 0 0 0 6 0
12 32 0 0 0 0 0 0 26 0 0 1 0 0 0 72 3
13 32 54 0 3 0 0 0 16 0 0 2 0 14 0 87 1
14 10 48 0 6 7 0 0 25 1 0 5 0 61 1 46 0
15 27 1 1 0 8 0 0 78 17 0 4 1 16 8 74 2
16 0 0 11 4 3 0 0 60 4 0 61 0 1 66 14 1
17 0 1 0 19 17 0 0 10 0 0 26 0 0 0 15 0
18 0 0 2 0 1 0 0 3 0 0 12 0 0 0 5 0
19 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0
20 0 0 1 0 0 0 0 0 0 0 0 0 0 5 0 0
21 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0
22 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
- Column one denotes the CDR3 length that were observed in rearrangements
containing the TRBV11-2*03 gene. Each of the following columns contains
the observance count for TRBJ genes that were observed in rearrangements
with TRBV11-2*03 gene and the CDR3 length of column one. So for example
the were 66 rearrangements observed containing TRBV11-2*03 and TRBJ2-6*01
and a CDR3 length of 16 amino acids.
Note:
TCRViz needs TR[A/B]J gene reference sequences (the same .fna file as used for TCRProfiler analysis) to visualize the repertoire and sorts then TR[A/B]J
gene entries in each fasta entry in lexicographic order of the TR[A/B]J gene names.
|
|
