ting - T cell receptor interaction grouping
Project description
ting
ting - T cell receptor interaction grouping
Synopsis
ting [options]
Options
Required Input
The user must provide a list of CDR3b sequences.
For compatibility reasons the tab seperated table of TCR sequences required for gliph is supported, too.
--tcr_sequences tcr_sequences The format of the table is tab delimited, expecting only the first
column. The header is optional, but if included only use column
names as shown in the example.
--kmer_file K-MER_FILE The k-mer file holds all 2-, 3- and 4-mers considered for local
clustering. If file does not exist it will automatically be
generated.
--reference Reference file used for simulation of sample sets.
Example:
CDR3b TRBV TRBJ CDR3a TRAV TRAJ Sample-ID
CAADTSSGANVLTF TRBV30 TRBJ2-6 CALSDEDTGRRALTF TRAV19 TRAJ5 09/02171
CAATGGDRAYEQYF TRBV2 TRBJ2-7 CAASSGANSKLTF TRAV13-1 TRAJ56 03/04922
CAATQQGETQYF TRBV2 TRBJ2-5 CAASYGGSARQLTF TRAV13-1 TRAJ22 02/02591
CACVSNTEAFF TRBV28 TRBJ1-1 CAGDLNGAGSYQLTF TRAV25 TRAJ28 PBMC8631
CAGGKGNSPLHF TRBV2 TRBJ1-6 CVVLRGGSQGNLIF TRAV12-1 TRAJ42 02/02071
CAGQILAGSDTQYF TRBV6-4 TRBJ2-3 CATASGNTPLVF TRAV17 TRAJ29 09/00181
CAGRTGVSTDTQYF TRBV5-1 TRBJ2-3 CAVTPGGGADGLTF TRAV41 TRAJ45 02/02591
CAGYTGRANYGYTF TRBV2 TRBJ1-2 CVVNGGFGNVLHC TRAV12-1 TRAJ35 01/08733
Optional Input
--use_structural_boundaries If set, the first and last three amino acids will be included
in kmer counting and global clustering.
--no_global No global clustering will be performed.
--no_local No local clustering will be performed.
--simulations Number of simulations that will be done for motif preprocessing.
Default is 1000.
--min_kmer_occurence Only kmers which occure at least min_kmer_occurences times in the
sequence sample set will be taken in account. Default is 3.
--max_p_value Only kmers with p_value < max_p_value will be used for clustering
--cores Number of cores used for multiprocessing. Multiprocessing is done
during sample set simulation. Default: 1
--stringent_filtering Only TCRs starting with a cystein and ending with phenylalanine will be
used (IGMT definition of CDR3 region). Default: False
Project details
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