resequcing analysis

A typical flow of resequencing analysis with reference is shown in the figure below

Two way to run:

multi-parameter way

ngspipedb runpipe ngspipe-run-resequencing -n ngspipe-resequencing --resultdirname result -d ../test_pipeline --genomeFasta ../testdata_ngspipe-rnaseq-basic/genome/chr19.fa --genomeAnno ../testdata_ngspipe-rnaseq-basic/genome/GRCm38.83.chr19.gtf --samplefile ../testdata_ngspipe-rnaseq-basic/rawdata/sample.csv --rawreadsdir ../testdata_ngspipe-rnaseq-basic/rawdata --snaketype p --readsprefix _R{}.fq.gz -j 1

ngspipe-run-resequencing your project name
-n ngspipe-resequencing pipeline name
-d ../test_pipeline working directory
--genomeFasta ../testdata_ngspipe-rnaseq-basic/genome/chr19.fa give a genome fasta file path, see file format fasta
--genomeAnno ../testdata_ngspipe-rnaseq-basic/genome/GRCm38.83.chr19.gtf give a genome annotaion file path gtf/gff
--samplefile ../rawdata/sample.csv give a sample file path, which has one column
--rawreadsdir ../testdata_ngspipe-rnaseq-basic/rawdata raw reads directory
--snaketype p run pipeline and print all shell command
--readsprefix _R{}.fq.gz this will find sample_R1.fq.gz and sample_R2.fq.gz automate
-j 1 cpu number

use configfile way

start a project in current directory:

ngspipedb startproject ngspipe-run-resequencing2 -n ngspipe-resequencing -d ../test_pipeline

PROJECTNAME: ngspipe-run-resequencing
pipeline: ngspipe-resequencing

tree ngspipe-run-resequencing

├── database
├── genome
├── ngsdb_config.yaml
├── ngspipe_config.yaml
└── rawdata
    └── sample.csv
3 directories, 3 files

copy your file to directory:

├── database
├── genome
│   ├── GRCm38.83.chr19.gtf
│   ├── chr19.fa
│   └── chr19.fa.fai
└── rawdata
    ├── control-0_R1.fq.gz
    ├── control-0_R2.fq.gz
    ├── control-1_R1.fq.gz
    ├── control-1_R2.fq.gz
    ├── control-2_R1.fq.gz
    ├── control-2_R2.fq.gz
    ├── sample.csv
    ├── treated-0_R1.fq.gz
    ├── treated-0_R2.fq.gz
    ├── treated-1_R1.fq.gz
    ├── treated-1_R2.fq.gz
    ├── treated-2_R1.fq.gz
    └── treated-2_R2.fq.gz

genome: the genome file
rawdata: resequencing data

modify configfile file ngspipe-run-resequencing/ngspipe_config.yaml:

#---------------------------
# medicago tnt1
#---------------------------

## 1.reference ##
genomeAnno_path: "genome/GRCm38.83.chr19.gtf" # gene annotation file, can be gtf or gff format
genomeFasta_path: "genome/chr19.fa" # genome sequence, fasta format

## 2.raw reads data ##
sample_path: "rawdata/sample.csv" # sample file
rawreads_dir: "rawdata" # sample file directory
read1Suffix: "_R1.fq.gz" # fastq suffix, read1
read2Suffix: "_R2.fq.gz"

## 3.output directory ##
results_name: "results"

## 4.notice ##
# if the string is 'nobody', ngspipe will not send email
# modify 'noboby' to 'xxx@qq.com' or 'xxx@qq.com,yyy@qq.com' to send email
email_addr: 'nobody'

# choose where to stop your pipeline
target: all #

#----------------------------------
# Configuration for sampling data
#----------------------------------

# for test the pipe, you can choose to the part of the input file
# which sampling method do you want to use?
sampling_method: links # links or head or tail or seqkit_number or seqkit_proportion
# Default is links (ues the whole data of sample); head (use first sampling_range line in every sample),tail (use last sampling_range line in every sample); seqkit_number (number of reads); seqkit_proportion (percentage of reads)
# and how many reads file line or reads number or reads proportion do you want to use?
sampling_value: 80000 # for head and tail, this value is line number; for number, this value is reads number; for proportion, this value is percentage

samples_num: all # all or interger
# Default is all (use all samples), give a sample number, must less than real sample number, for example 6

#----------------------------------
# Configuration for Quality Control
#----------------------------------
# which qc method do you want to use?

qc_method: trim-galore # trim-galore or trimmomatic or fastqc

#----------------------------------
# Configuration for Genome cut
#----------------------------------
# which part of genome do you want to use?
sub_genome: all # all (whole genome) or chr1:10000-20000 (seq name:start position-end position) or chr1 (seq name)

run command:

ngspipedb runpipe ngspipe-run-resequencing -n ngspipe-resequencing -c ngspipe-run-resequencing/ngspipe_config.yaml -j 1