- TRUST4
Github link. You can install it from Github source or if you have conda, just run conda install -c bioconda trust4
In a HPC environment, run sbatch trust4batch.sh output_dir bam_files_dir reference_file to submit your job to your HPC cluster. Make sure to replace output_dir, bam_files_dir, and reference_file with the appropriate values for your specific use case.
output_dir : It's where you store the output folders and files from running trust4
bamfiles_dir: It's the directory of where you store the bamfiles
reference_file: This is just hg38_bcrtcr.fa, unless you have a custom file in place of it.
Else just run ./trust4run.sh output_dir bam_files_dir reference_file.
In a HPC environment, run sbatch trust4_run_fastq_batch.sh path_to_fastq_files output_dir reference_file to submit your job to your HPC cluster. Make sure to replace these arguments with the appropriate values for your specific use case.
The trust4run.sh script is optimised to deal with avoiding any sort of computation on the data files in UQ HPC storage, therefore there is an extra step of copying the data files to $TMPDIR beforehand. You can modify them
if your data files is stored elsewhere that does not have any restrictions.
Not all files from TRUST4 output will be used. The file from the output that needs particular attention is file with the suffix of filename_airr.tsv. You should find the corrospending files in the output (sub)directories that you specified.
We only need certain columns the files and only want assembled TRB gene locus type. Therefore we will run trim_trust4_output.sh. The output files will be in the suffix naming filename_extracted.tsv in the same respective directories in which the output files from running TRUST4 is generated.