ROP output details (IgBLAST )

antibodyProfile directory

Note: This is relevant to versions of ROP using IgBLAST (versions <1.0.6). Starting with ROP v1.0.6, we we have switched from IgBLAST to ImReP to profile B and T cell receptor repertoires. ImReP shows superior accuracy compared to existing tools (see our manuscript “Profiling adaptive immune repertoires across multiple human tissues by RNA Sequencing” available at bioRxiv).

This directory contains the output of Step 5. B and T lymphocytes profiling.

Starting from release ROP v1.0.6 we are using accurate in-house tool to detect reads spanning V(D)J recombination to quanity individual immune response.

It contains a separate directory for B cell receptors (BCR) : BCR directory and a separate directory for T cell receptor (TCR) : TCR directory.

BCR directory contains:

• IGH a directory for immunoglobulin heavy locus profile
• IGK a directory for immunoglobulin kappa locus
• IGL a directory for immunoglobulin lambda locus profile

TCR directory contains:

• TCRA a directory for T cell receptor alpha locus
• TCRB a directory for T cell receptor beta locus
• TCRG a directory for T cell receptor gamma locus
• TCRD a directory for T cell receptor delta locus

Reads spanning antigen receptor gene rearrangement in the variable domain are identified using IgBLAST. IgBLAST reports alignment of the reads to the variable (V) gene, the diversity (D) gene and the joining (J) gene, or the recombination of those. Reads alignment is saved into the _igblast.csv (modified tabular output format 6).

n	id	What does it mean?
0	VDJ	gene segment
1	qseqid	read name
2	sseqid	reference genome
3	pident	percentage of identical matches
4	length	alignment length
5	mismatch	number of mismatches
6	gapopen	number of gap openings
7	qstart	start of alignment in query
8	qend	end of alignment in query
9	sstart	start of alignment in subject
10	send	end of alignment in subject
11	evalue	expect value
12	bitscore	bit score

An example of the unmapped read aligned to the immunoglobulin heavy variable 1-46 gene (IGHV1-46)

V       SRR1146076.56325        IGHV1-46*01     93.67   79      5       0       0       1       79      203     281     7e-27     109