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. TRUST performs de novo assembly on the hypervariable complementarity-determining region 3 (CDR3) and reports contigs containing the CDR3 DNA and amino acid sequences. TRUST then realigns the contigs to IMGT reference gene sequences to report the corresponding variable (V) or joining (J) genes. TRUST supports both single-end and paired-end sequencing data with any read length. Questions or suggestions should be addressed to Bo Li (Bo.Li@UTSouthwestern.edu) or Shirley Liu (email@example.com). TRUST is developed by Bo Li, Jian Zhang and Xihao Hu in Shirley Liu lab, with all rights reserved.
Please join our google group https://groups.google.com/forum/#!forum/trusttcr/new to address all questions or concerns.
Download the latest version of TRUST from “https://bitbucket.org/liulab/trust”
Unzip the source code and go into the directory by using the following command:
tar xvzf trust-*.tar.gz
Invoke the setup script:
python setup.py install
If you don’t have permission to the standard directory or you don’t want to install it as a standard part of your local Python installation, you can use the following command instead:
python setup.py install —-user
or: python setup.py install --home=<dir>
more details: https://docs.python.org/2/install/
Dependency for TRUST is shown in requirements.txt, which can be automatic installed by using the above command.
## Input files
TRUST takes BAM files as input. Please make sure that each BAM is paired with its index file, ending with .bam.bai BAM file could be aligned to hg19 or hg38 human reference genome
## Input modes
TRUST supports 3 input modes, to accommodate multiple file inputs.
-d option processes all the BAM files in a given directory
-F option processes all the files listed in a given file list (in a txt file)
-f option processes a single BAM file
## General usage
trust -f YOUR_BAM_FILE.bam -g hg19
trust -f YOUR_BAM_FILE.bam -g hg19 -B
trust -f YOUR_BAM_FILE.bam -g hg19 -B -L
## Result fields of fasta info line File name 10 digits random ID TCR genes and locations (based on mapped reads) Estimated clonal frequency: the number of reads used to assemble the contig divided by contig length Contig length Number of reads in the TCR regions TCR gene (based on alignment to IMGT reference genes) CDR3 amino acid sequence Minus log e-value: E-value for IMGT reference alignment CDR3 DNA sequence
## Version history
Jan 24, 2018 Version 3.0
support mm10 (-g mm10) Add tcr partial sequence extension module (-E option) and IMGT gene coverage report(-c option) fix bugs in dna sequence report, format output
Jan 17, 2018 Version 2.5.3 Add post-processing module (format_trust_output.py) to parse and trim the TRUST fasta output
Nov 17, 2017 Version 2.5.2 Add BCR light chain analysis (-B -L option) Use the SIMD version of local alignment to gain a 10x speedup
May 26, 2017 Allow input soft-clipping reads
Feb 24, 2017 Version 2.4.1 Allow input BAM file aligned to hg38 human reference genome. trust -f YOUR_BAM_FILE.bam -g hg38
Feb 20, 2017 Version 2.4.0 Add installation method, make it easy to install and use. Complete a structured package by reorganizing the data and program.
Feb 02, 2017 Version Change FindDisjointCommunities to non-recursive to avoid Python recursion depth limit.
Jan 27, 2017 Version Fix a bug in reads compare function CompareSuffixByBit. Add C++ extension getOverlapInfo.so to CompareSuffixByBit and CompareSuffixByBitSeq, speeding up them by 5x. Add Multithreading process in GetReadsOverlapByGene and GetReadsOverlapByGene_SE.
Nov 21, 2016 Version Change GetSeqOverlap and GetSeqOverlap_SE into linear scale
Nov 08, 2016 Add multiple-variable gene assignment force TRUST to screen for all vgene assignment, slow.
May 31, 2016 Add single end component