Trust4

Introduction

Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/trust4
Home page: https://github.com/liulab-dfci/TRUST4

Versions

  • 1.0.7

Commands

  • run-trust4

  • BuildDatabaseFa.pl

  • BuildImgtAnnot.pl

  • trust-airr.pl

  • trust-barcoderep.pl

  • trust-simplerep.pl

  • trust-smartseq.pl

Module

You can load the modules by:

module load biocontainers
module load trust4

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run trust4 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=trust4
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers trust4

run-trust4 -b mapped.bam -f hg38_bcrtcr.fa --ref human_IMGT+C.fa