Software: Tcr Receptor Utilities for Solid Tissue (TRUST) 4
Description
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.
Available Versions
| Unspecified: | 1.0.7 |
|---|
BioContainers: https://biocontainers.pro/tools/trust4
Home page: https://github.com/liulab-dfci/TRUST4
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
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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