liulab-dfci / TRUST4

TCR and BCR assembly from RNA-seq data

liulab-dfci/TRUST4 Issues

Different outputs of 10x scData-TCR between MiXCR and TRUST4
Updated 2 months ago20
Deconvolution of 3' 10x genomics GEX data with TRUST4
Updated 2 months ago1
trust-smartseq.pl Output
Closed 2 months ago11
CDR3 clustering among multiple samples (bulk RNA-seq)
Closed 2 months ago4
the rule of barcode correction
Updated 2 months ago55
Permission of commercial use
Closed 2 months ago6
failed: 139 at ./run-trust4 line 55.
Updated 2 months ago13
UMI count question
Closed 3 months ago25
How to use fastq-extractor to deal with paired-UMI sequencing data in trust4 suite
Updated 3 months ago10
should the best record of multiple records be used for downstream analysis?
Closed 3 months ago4
failed: 256 at ./run-trust4 line 55.
Updated 3 months ago7
empty cell_id column in airr file from 10x Genomics data
Updated 3 months ago5
Differences in counts compared to MIXCR results, and out-of-frame CDR3 handling
Updated 3 months ago8
Question about paired-end 10x genomics data
Closed 3 months ago2
Best way to run TRUST4 on SMARTer data
Closed 3 months ago16
Understanding of the output files
Updated 4 months ago3
Merge FASTQs of same sample before TRUST4
Closed 5 months ago8
Description of columns in trust4_report.tsv, specifically column C
Closed 5 months ago2
How to get the sequence of C region？
Updated 5 months ago5
full-length amino acid sequence
Updated 5 months ago7
TRUST4 fails with error 139 at ./run-trust4 line 54
Updated 5 months ago16
Segmentation fault in annotation stage
Closed 6 months ago3
Issue with Running BuildDatabaseFa.pl Script for TCR and BCR Analysis in Vicugna pacos (Alpaca)
Updated 7 months ago2
Question about lambda and kappa
Updated 7 months ago2
How TRUST4 defines clones
Closed 7 months ago2
Buffer overflow detected
Closed 7 months ago4
TRUST4 on 10X 3' sequencing output question
Closed 7 months ago1
Question about read aggregation by barcode
Updated 7 months ago3
Problem with TRUST4 BCR entropy calculation
Updated 7 months ago1
No overlap between the barcodes from TRUST4 and those in the barcodes.tsv.gz
Updated 7 months ago1
Confusion with count and frequency in results.tsv
Closed 8 months ago7
How are CDR3 scores calculated?
Closed 8 months ago2
Unrecognized option '--UMI--barcode': annotatorArgs improperly concatenated
Updated 8 months ago1
sample1_toassemble_bc.fa failed: 9 at /usr/local/bin/run-trust4 line 54
Closed 8 months ago5
almost same CDR3 nucleotides from different assemblies
Updated 8 months ago8
TRUST 4 barcode parameter for the bam files
Closed 10 months ago7
all contigs in the TRUST4 result are high confident?
Updated 8 months ago1
How is `cid_full_length` assigned?
Updated 9 months ago3
AIRR file
Closed 9 months ago8
Question about outputs
Closed 9 months ago2
Inquiry about the Usage of TRUST4 in 10X 3' scRNA-seq Data Analysis
Updated 9 months ago1
How are Consensus IDs Created?
Closed 9 months ago9
Missing J sequences
Updated 9 months ago1
Issue annotating assemblies: Segmentation fault:11 and error 35584 at ./run-trust4 line 54.
Closed 9 months ago7
[Question] How to run using 10X data?
Closed 9 months ago7
How to deal with sequencing depths in multiple samples.
Updated 9 months ago3
the problem of -u(--abnormalUnmapFlag from wrapper)
Closed 10 months ago7
What is the corresponding nucleotide weight mean in the trust_final.out file?
Closed 10 months ago2
Sample normalization and BCR SHM calculation
Closed 10 months ago4
Use TRUST4 on selected RNAseq data
Closed 10 months ago4