Skip to content

archaemenes/KIR_typing

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

12 Commits
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

KIR typing with KPI and KIR_graph

KIR typing using KPI https://github.com/droeatumn/kpi and KIR_graph https://github.com/linnil1/KIR_graph for haplotypes, copy number and allele level resolution with paired end short read data.

Download dependencies

For KPI install Java, Groovy, Nextflow, Docker, and Git. Create accounts in GitHub and Docker Hub. Add 'docker.enabled = true' and 'docker.fixOwnership = true' to your Nexflow configuration at $HOME/.nextflow/config (refer https://github.com/droeatumn/kpi)

For KIR_graph install python >= 3.10, muscle >= 5.1, histat2 >= 2.2.1, samtools >= 1.15.1, bwa-mem > 0.7.17 (refer https://github.com/linnil1/KIR_graph)

Choose workflows

You can choose between the two work flows KPI or KIR_graph KPI_pipeline.sh for KPI requires to run the scripts in the following order:

bash download_refernces.sh 
bash KPI_pipeline.sh 

Make sure to set the environmental variables as given in the scripts:

WORKDIR='/pathTo/workDir/'
OUTDIR='/pathTo/outDir' 
OUT_PREFIX='KIR_graphOut'
READ1='/pathTo/NK-WGL_R1_val_1.fq.gz'
READ2='/pathTo/NK-WGL_R2_val_2.fq.gz'
THREADS=16

For the KIR_GraphPipeline.sh for KIR_graph requires to run the following scripts and set the environmental variables:

cd $WORKDIR

wget -c https://github.com/rcedgar/muscle/releases/download/5.1.0/muscle5.1.linux_intel64
mv muscle5.1.linux_intel64 muscle
echo "alias muscle=${WORKDIR}/muscle" >> ~/.bashrc
source ~/.bashrc

conda create -n KIR_typing python==3.12
conda install -c "bioconda/label/cf201901" hisat2 -n KIR_typing
conda install -c bioconda samtools -n KIR_typing
conda install -c bioconda bwa -n KIR_typing
conda install -c conda-forge docker -n KIR_typing
conda install -c anaconda git -n KIR_typing
conda activate KIR_typing

Run bash KIR_GraphPipeline.sh to obtain copy number and allele level information.

Getting the expression level information

Install dependencies bedtools, samtools for file processing, STAR rnaSeq alignment, TrimGalore for trimming adapters (required for initial steps of WGS analysis too). Run bash expression.sh with results in ${OUTDIR}/${OUT_PREFIX}_onlyKIRs_NormalizedByTPM.tsv

Analysing results

For KIR_graph To find the nucleic acid sequences of the allele variants obtained from the analysis:
find ~/ -name "KIR_v*"

Copy number results: cat ${OUTDIR}/${OUT_PREFIX}.cn.tsv

Allele level typing results: cat ${OUTDIR}/${OUT_PREFIX}.allele.tsv

For KPI Haplotype level typing: cat ${OUTDIR}/Knew_prediction.txt

About

KIR typing using short paired end data.

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published