Comments (1)
Hi,
It seems that the sequences in the table do not fully cover the V gene in many cases and sometimes include either a complete or partial CDR3. To use these sequences, you should first align them to the genome and, using RSS sequences, extract the complete V and J genes. Then, create FASTA files with a list of genes for each gene segment, like this:
>IGHV12-348
GATGCTGGAGTTATCCAGTCACCCCGCCATGAGGTGACAGAGATGGGACAAGAAGTGACTCTGAGATGTAAACCA
ATTTCAGGCCACAACTCCCTTTTCTGGTACAGACAGACCATGATGCGGGGACTGGAGTTGCTCATTTACTTTAAC
AACAACGTTCCGATAGATGATTCAGGGATGCCCGAGGATCGATTCTCAGCTAAGATGCCTAATGCATCATTCTCC
ACTCTGAAGATCCAGCCCTCAGAACCCAGGGACTCAGCTGTGTACTTCTGTGCCAGCAGTTTAGC
To create a TRA library, use a command similar to the one below:
mixcr buildLibrary \
--v-genes-from-fasta v-genes.TRA.fasta \
--v-gene-feature VRegion \
--j-genes-from-fasta j-genes.TRA.fasta \
--c-genes-from-fasta c-genes.IGH.fasta \ # optional
--chain TRA \
--taxon-id 9823 \
--species pig \
pig-TRA.json.gz
Next, merge this library with IMGT reference for MiXCR:
mixcr mergeLibrary \
pig-TRB.json.gz \
imgt.202214-2.sv8.json.gz \
my-custom-imgt.json.gz \
Then use the library like this:
mixcr analyze generic-amplicon \
--library my-custom-imgt \
--species pig \
--rna \
--rigid-left-alignment-boundary \
--floating-right-alignment-boundary C \
input_R1.fastq.gz \
input_R2.fastq.gz \
output
We also have a dedicated tutorial on this topic.
from mixcr.
Related Issues (20)
- Nanopore Data HOT 4
- Unexpected behavior when running mixcr analyze from a script HOT 2
- Artificial Diversity Correction HOT 1
- Artificial gaps in reported amino acid sequences HOT 2
- UMI with Nanopore Data HOT 1
- Mixcr to VDJtools HOT 1
- TotalReads count not set HOT 10
- Number of aligned reads distinct between preset rna-seq and generic-amplicon-with-umi HOT 1
- UMI-based error correction HOT 1
- RefineTagsAndSort HOT 1
- For detection of somatic hypermutation (SHM) ? HOT 1
- postanalysis NullPointerException HOT 9
- Somatic hypermutation analysis HOT 1
- Analysis of single chain Fragment variable (scFv) HOT 1
- Error exportPlots shmTrees - Duplicate library: repseqio.v4.0_with_found_alleles:10090 HOT 2
- transitioning from postanalysis to exportPlots HOT 1
- Somatic Hypermutation Status of IGHV status HOT 2
- Question about filtering reads prior to Mixcr HOT 1
- Preset for long-read RNAseq with cell barcode HOT 1
- How to perform MiXCR on my spatial TCR data HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from mixcr.