ImReP: rapid and accurate profiling of the adaptive immune repertoires from regular RNA-Seq data.
ImReP is a novel computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data. It is able to efficiently extract TCR- and BCR-derived reads from RNA-Seq data. ImReP can also accurately assemble the complementary determining regions 3 (CDR3s), the most variable regions of B and T cell receptors, and determine their antigen specificity.
References:
- S.Mangul, I.Mandric, H.Taegyun Yang, N.Strauli, D.Montoya, J.Rotman, W.Van Der Wey, J.R.Ronas,
B.Statz, D.Yao, A.Zelikovsky, R.Spreafico, S.Shifman, N.Zaitlen, M.Rossetti, K.M.Ansel, E.Eskin
Profiling adaptive immune repertoires across multiple human tissues by RNA Sequencing,
bioRXiv preprint first posted online Nov. 22, 2016; doi: http://dx.doi.org/10.1101/089235.
Documentation
Important Notes
- Module Name: ImReP (see the modules page for more information)
- Unusual environment variables set
- IMREP_HOME installation directory
- IMREP_BIN executable directory
- IMREP_SRC source code directory
- IMREP_DATA sample data directory
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive --mem=4g
[user@cn3316 ~]$ module load imrep
[+] Loading singularity 4.0.1 on cn3316
[+] Loading imrep 0.8
[user@cn3316 ~]$ imrep.py -h
usage: python2 imrep.py [-h] [--fastq] [--bam] [--chrFormat2] [--hg38]
[-a ALLREADS] [--digGold] [-s SPECIES] [-o OVERLAPLEN]
[--noOverlapStep] [--extendedOutput] [-c CHAINS]
[--noCast] [-f FILTERTHRESHOLD]
[--minOverlap1 MINOVERLAP1]
[--minOverlap2 MINOVERLAP2] [--misMatch1 MISMATCH1]
[--misMatch2 MISMATCH2]
reads_file output_clones
optional arguments:
-h, --help show this help message and exit
Necessary Inputs:
reads_file unmapped reads in .fasta (default) or .fastq (if flag
--fastq is set) or .bam (if --bam or --digGold is set)
output_clones output file with CDR3 clonotypes
Optional Inputs:
--fastq a binary flag used to indicate that the input file
with unmapped reads is in fastq format
--bam a binary flag used to indicate that the input file is
a BAM file mapped and unmapped reads
...
Advanced Inputs:
--minOverlap1 MINOVERLAP1
minimal overlap between the reads and A) the left part
of V gene (before C amino acid) and B) the right part
of J gene (after W for IGH and F for all other
chains), default is 4
--minOverlap2 MINOVERLAP2
minimal overlap between the reads and A) the right
part of V gene (after C amino acid) and B) the left
part of J gene (before W for IGH and F for all other
chains), default is 1
...
[user@cn3316 ~]$ suffix_tree.py
SIMPLE TEST
leaf: "mississippi$" : "mississippi$"
leaf: "ississippi$" : "ssippi$"
leaf: "issippi$" : "ppi$"
leaf: "ippi$" : "ppi$"
leaf: "i$" : "$"
leaf: "ssissippi$" : "ssippi$"
leaf: "ssippi$" : "ppi$"
leaf: "sissippi$" : "ssippi$"
leaf: "sippi$" : "ppi$"
leaf: "ppi$" : "pi$"
leaf: "pi$" : "i$"
leaf: "$" : "$"
inner: "ssi"
inner: "i"
inner: "si"
inner: "i"
inner: "s"
inner: "p"
inner: ""
done.
GENERALISED TEST
----------------------------------------------------------------------
0 [0:1] x |x|abxa
0 [3:4] x xab|x|a
1 [3:4] x bab|x|ba
----------------------------------------------------------------------
0 [1:4] abx x|abx|a
1 [1:4] abx b|abx|ba
----------------------------------------------------------------------
0 [1:2] a x|a|bxa
1 [1:2] a b|a|bxba
0 [4:5] a xabx|a|
1 [5:6] a babxb|a|
----------------------------------------------------------------------
0 [2:4] bx xa|bx|a
1 [2:4] bx ba|bx|ba
----------------------------------------------------------------------
0 [2:3] b xa|b|xa
1 [2:3] b ba|b|xba
1 [0:1] b |b|abxba
1 [4:5] b babx|b|a
======================================================================
----------------------------------------------------------------------
0 [1:4] abx x|abx|a
1 [1:4] abx b|abx|ba
----------------------------------------------------------------------
0 [2:4] bx xa|bx|a
1 [2:4] bx ba|bx|ba
======================================================================
done.
End the interactive session:
[user@cn3316 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$