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Running TRAPeS on other genomes

TRAPeS can be used for any genome and any organism, as long as the genomic annotations for the V/J/C segments are available. In order to run TRAPeS on genomes besides mm10, hg19 or hg38, the user must create those annotations and provide the correct value for the '-genome' parameter.

Instructions to create new annotations for TRAPeS (see existing genome folders for examples):

Under the Data folder, create a new folder. The name of the folder is the value you will provide the ‘-genome’ parameter. The folder should include only these 4 files:

  1. *.gene.id.mapping.TCR.txt (file name must end with ‘gene.id.mapping.BCR.txt’): A file with no header and two columns: first column is the ID of the V/J/C segment as it appears in the *.TCR.bed file (see below) and the second column is the name of the segment (e.g. TRBV20-1, TRAJ54 etc.). This file can be created, for example, from the ensemble download page, selecting only Transcript stable ID and Gene name, and then filtering the file to include only V/J/C segments. No need to include the beta chain ‘D’ segment annotations.
  2. *.TCR.bed: Genomic annotations in bed format of the V/J/C segments. Note that TRAPeS will only attempt to reconstruct TCRs from the V and J segments in this file.
  3. *.TCR.fa: A fasta file with the sequences of all V/J/C segments (can be generated from the TCR.bed file with the bedtools getfasta commend).
  4. *.conserved.AA.txt: A file with two columns and no header. The first column includes the name of the V/J segment (same name as in the *.gene.id.mapping.TCR.txt file). The second column includes the amino acid sequence of the protein up to the conserved amino acid from which the CDR3 is defined. I.e, for V segments it includes the amino acid sequence of the protein up until the conserved Cysteine at position 104 (including the Cysteine). For the J segments it has the amino acid sequence from the conserved W/F amino acid until the end of the J segment. The file needs to include the V and J sequences from all chains (alpha and beta).
    One way to generate this file is by copying the protein sequences from the “Protein display” page of the “IMGT repertoire” (link), and to manually arrange the sequences from all chains to fit the format above.