perturb_processing

The raw data management and processing scripts used for https://perturbatlas.kratoss.site/ database

Code structure

• db: contains database structure file for raw data and processing task management
• src: contains separate scripts to execute software for quality control, alignment and quantification software etc.
• R: contains separate scripts to execute differential analysis, enrichment etc.
• config.ini: contains the basic configuration for database
• adapters: contains PE and SE adapters retrieved from https://github.com/usadellab/Trimmomatic/tree/main/adapters
  • PE.fa: merged by NexteraPE-PE.fa, TruSeq2-PE.fa, TruSeq3-PE-2.fa, TruSeq3-PE.fa
  • SE.fa: merged by TruSeq2-SE.fa, TruSeq3-SE.fa

Prepare environments

1. basic python environments

poetry install

pooetry run python main.py --help

2. R packages required

• clusterProfiler
• data.table
• DESeq2
• dplyr
• DRIMSeq
• glue
• GO.db
• pbapply
• stageR
• stringr
• reshape2
• tidyr
• rjson
• tximport

3. the annotation database for multi-species required by enrichment analysis

The content of 03.generate_pair/annotation.csv required by R/enrichment_split_run.R.

• First column is the short scientific name for species.
• Second column is the R packages or absolute path to generated Gene_go_inf.Rds by R/prepare_go_inf.R script.
• Third column is the key type used by clusterProfiler.

AraAth,org.At.tair.db,TAIR
CaeEle,org.Ce.eg.db,ENSEMBL
DanRer,org.Dr.eg.db,ENSEMBL
DroMel,org.Dm.eg.db,ENSEMBL
EscCol,org.EcK12.eg.db,SYMBOL
GalGal,org.Gg.eg.db,ENSEMBL
HomSap,org.Hs.eg.db,ENSEMBL
MusMus,org.Mm.eg.db,ENSEMBL
OrySat,OrySat/release52/Gene_go_inf.Rds,IG
RatNor,org.Rn.eg.db,ENSEMBL
SacCer,org.Sc.sgd.db,ENSEMBL
SolLyc,SolLyc/release52/Gene_go_inf.Rds,IG
SusScr,org.Ss.eg.db,SYMBOL

4. others tools

please follow the official tutorials to install required software and make sure executables properly pleased in your $PATH.

• trimmomatic
• star
• salmon
• rmats
• splicetools
• etc.

Note: for trimmomatic, please make sure the java is properly installed, and the jar file of trimmomatic placed under adapters directory.

Usage

python main.py --help

NAME
    main.py

SYNOPSIS
    main.py COMMAND

COMMANDS
    COMMAND is one of the following:

     splice
     rmats
     download
     star
     salmon
     sleuth
     trimmomatic

The usage for different subcommands:

python main.py download --help

NAME
    main.py download

SYNOPSIS
    main.py download <flags>

FLAGS
    --server=SERVER
        Type: str
        Default: '1130'
    -o, --outdir=OUTDIR
        Type: Optional[Optional]
        Default: None
    -a, --aria2c=ARIA2C
        Type: bool
        Default: False
    -g, --give_up=GIVE_UP
        Type: bool
        Default: False
    --species=SPECIES
        Type: Optional[Optional]
        Default: None