Exogenous TE insertion

• ITIS: tool to Identify TE Insertion Sites in genome
• https://github.com/Chuan-Jiang/ITIS
• https://pubmed.ncbi.nlm.nih.gov/25887332/

Two way to run:

multi-parameter way

ngspipedb runpipe ngspipe-tnt-medicago -n ngspipe-tnt --resultdirname result -d ../ --genomeFasta ../genome/scf003.fa --genomeAnno ../genome/scf003.sorted.gff --samplefile ../rawdata/sample.csv --rawreadsdir ../rawdata --snaketype p --reads_prefix _R{}_paired.fastq.gz -j 20

• ngspipe-tnt-medicago your project name
• -n ngspipe-tnt pipeline name
• --genomeFasta ../genome/scf003.fa give a genome fasta file path, see file format fasta
• --genomeAnno ../genome/scf003.sorted.gff give a genome annotaion file path gtf/gff
• --samplefile ../rawdata/sample.csv give a sample file path, which has one column

use configfile way

1. start a project in current directory:

   ngspipedb startproject medicago_tnt_zhao -n ngspipe-tnt
   

   • PROJECTNAME: medicago_tnt_zhao
   • pipeline: ngspipe-tnt
   • tree medicago_tnt_zhao

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

2. copy your file to directory:

   ├── database
   │   ├── exogenous
   │   │   ├── medicago_mere1.fa
   │   │   └── medicago_tnt1.fa
   ├── 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
   

   • database/exogenous: the directory of exogenous sequence
   • genome: the genome file
   • rawdata: resequencing data

3. modify configfile file medicago_tnt_zhao/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
   exogenous_seq_path: "database/exogenous/medicago_tnt1.fa" # medicago_mere1.fa or medicago_tnt1.fa
   
   ## 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)
   

4. run command:

   ngspipedb runpipe medicago_tnt_zhao -n ngspipe-tnt -c medicago_tnt_zhao/ngspipe_config.yaml -j 1