Dependencies

software

    MAFFT
    GMAP

Python Modules

    outlier-utils

Installation

    cd /path/to/install
    git clone https://github.com/Chaiyuangungun/PanMarker.git
    chmod +x PanMarker/get_promoter_and_cds.py
    echo 'export PATH=/path/to/install/PanMarker:$PATH' >> ~/.bash_profile
    source ~/.bash_profile

Usage

1、Mapping reference cds to all genomes in pan-genome

    # For each sample, run command below
    gmap_build -D . -d DB genomeN.fasta
    gmap -D . -d DB -f 2 -n 1 -t 20 ref.cds > genomeN.gff3

2、Extract cds with gff3 file generated by gmap

    # For each sample, run command below
    ./get_promoter_and_cds.py genomeN.gff3 genomeN.fasta 2000 genomeN

3、Extract variants and extart variant sites associate with traits

    ls *.prm >prm.file 
    ls *.cds >cds.file

use cds file :

    python3 PanMarker.py -i cds.file -p trait.file -e FPKM.file -s cds -o prefix -g T\F【-t num -a person_cor】
            -i INPUTFILE, --inputfile  input file(cds or prm file list)
            -p PHE, --phe              phenotype file
            -e EXP, --exp              expression profile
            -s TYPE --type             file type, cds or prm
            -o OUTPUT, --output        output file prefix
            -g GRU, --gru              T or F,Ture or False, whether to perform phenotype outlier filtering
            -t THREAT, --threat        Number of threads (default=10）
            -a PERVALUE --pervalue     Pearson correlation coefficient(default=0.3)

trait.file :

    sample1 value1

    sample2 value2

    ...

    sampleN valueN

FPKM.file :

            gene1 gene2 gene3 ... geneN
   
    sample1 xx  xx  xx  ... xx

    sample2 xx  xx  xx  ... xx

    ...

    sampleN xx  xx  xx  ... xx

use prm file:

    python3 PanMarker.py -i prm.file -p FPKM.file -s prm -o prefix -g T\F【-t num】
            -i INPUTFILE, --inputfile  input file(cds or prm file list)
            -p PHE, --phe              expression profile
            -s TYPE --type             file type, cds or prm
            -o OUTPUT, --output        output file prefix
            -g GRU, --gru              T or F,Ture or False, whether to perform phenotype outlier filtering
            -t THREAT, --threat        Number of threads (int,default=10）
            -a PERVALUE --pervalue     Pearson correlation coefficient(float,default=0.3)

2、result

    prefix.result(all variant sites associate with phenotype)
            
    prefix.out(top 5% variant sites associate with phenotype)