Question 1

What data can I run through the Bulk TCR Detection pipeline?

Accepted Answer

T-cell receptor libraries delivered as raw paired-end FASTQs. The reference for each sample is set in the samplesheet, either human or mouse, and TRUST4 runs in the mode for amplicon-based TCR-seq libraries by default, which is the usual setup for targeted TCR sequencing.

Question 2

Can I mix human and mouse samples in one run?

Accepted Answer

Yes. Each sample carries its own reference in the samplesheet, so human and mouse libraries can sit in the same batch. FastQC still runs on both reads of every sample, and the repertoire summary lines all the samples up side by side, so a mixed batch stays readable.

Question 3

What comes back from a Bulk TCR Detection run?

Accepted Answer

Four things: per-sample AIRR-format and report tables in both full and productive-only versions, clonal abundances and TRA/TRB gene assignments, a cross-sample repertoire summary table, and one Bridge Horizon-branded MultiQC report for the experiment.

Question 4

What is the difference between the full tables and the productive-only tables?

Accepted Answer

TRUST4 reports every receptor it reconstructs, including rearrangements that are unlikely to encode a working receptor. The productive filter keeps those with a clean CDR3 amino acid sequence, the standard reading of a receptor predicted to be functional. Both sets come back, so a focused productive view and the complete result open side by side.

Question 5

What do clonal abundances and TRA/TRB gene assignments tell me?

Accepted Answer

Clonal abundance says how much of the repertoire each reconstructed clonotype accounts for, which is where an expanded population shows up. The TRA and TRB assignments record the receptor chains and genes behind each clonotype, so you can see which gene segments a sample is using alongside which clones are present.

Question 6

How do I read the MultiQC report?

Accepted Answer

Read quality and repertoire numbers arrive in one report, so the first pass is to compare samples against each other rather than opening a separate file for each one. Where a sample looks thin on clonotypes, or its read-quality results sit apart from the rest of the batch, that is the one to look at before drawing a conclusion from its repertoire.

Question 7

Is this the right pipeline for my data?

Accepted Answer

It is built for bulk TCR libraries sequenced as paired-end reads. Single-cell expression data from 10x Genomics is handled by the single-cell pipeline, and gene expression from bulk RNA-seq is handled by the bulk RNA-seq pipeline.

Bulk TCR Detection

Input

Output

From reads to repertoire

Why each step is here

FastQC

TRUST4

Productive TCR filter

Repertoire summary

MultiQC

What comes back

Bulk TCR Detection FAQ

Take the next step

Run it in Horizon

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