Prerequisites

1. Docker or conda
2. Java (version >= 1.7)
3. Nextflow (version >= 20.07.1.5413)
4. 7z sudo apt install p7zip-full p7zip-rar

Download

1. Download PipeOne

git clone https://github.com/nongbaoting/PipeOne.git

2. Download reference and testing data

Download one of the data sets below:

• google drive

• or Baidu Cloud Disk:

  Link: https://pan.baidu.com/s/1gbZR1LJAmuT_fmFY1UJ7sA

  Extraction code: 8fnl

Installation

Using docker

Pull down the PipeOne Docker image

docker pull nongbaoting/pipeone:latest

or use conda environment instead of docker

cd PipeOne/INSTALL
bash ./install.sh

To ensure a successful installation, we recommend that you run each command step by step in the shell script install.sh

Prepare reference index

Uncompressed reference data

7z x hg38_ref.7z
cd hg38_ref

Configuration

Modify the program configuration file PipeOne/conf/genomes.config, change the line below:

ref_directory = "" change to ref_directory = "/your/path/to/hg38_ref"

params {

  genomes {

    "hg38" {
        // the reference directory you need to specify
        ref_directory           = "/your/path/to/hg38_ref"

        // No need to change below
        species                 = "human"
        genome_build            = "hg38"

        // in the download files
        fasta                   = "${ref_directory}/hg38.fa"
        fasta_fai               = "${ref_directory}/hg38.fa.fai"
        gtf                     = "${ref_directory}/gencode.v32.gtf"
        ref                     = "${ref_directory}/hg38_ref.txt"
        genecode_gtf            = "${ref_directory}/gencode.v32.gtf"
        genecode_lncRNA_gtf     = "${ref_directory}/gencode.v32.long_noncoding_RNAs.gtf"

        lncpedia_gtf            = "${ref_directory}/lncipedia_5_2_hg38.addquotes.gtf"
        repeat_gtf              = "${ref_directory}/hg38_ucsc.repeat.gtf"
        retro_gtf               = "${ref_directory}/telescope_HERV_rmsk.hg38.v2/transcripts.gtf"
        sprint_repeat           = "${ref_directory}/sprint_hg38_repeat.txt"
        blacklisted             = "${ref_directory}/arriba_db/blacklist_hg38_GRCh38_2018-11-04.tsv.gz"
        cytobands               = "${ref_directory}/arriba_db/cytobands_hg38_GRCh38_2018-02-23.tsv"
        proteinDomains          = "${ref_directory}/arriba_db/protein_domains_hg38_GRCh38_2018-03-06.gff3"
        salmon_index_3UTR       = "${ref_directory}/apa_3UTR/gencode_v31/3utr"
        replace_SalmonIndex_ID  = "${ref_directory}/apa_3UTR/gencode_v31/fa_id_relate.txt"
        apa3utr                 = "${ref_directory}/apa_3UTR/gencode_v31/qapa_3utrs.gencode_V31.hg38.bed"
        utr_gtf                 =  genecode_gtf
        annovar_data_dir        = "${ref_directory}/annovar_db"

        // generate by prepare_ref.nf
        star_index              = "${ref_directory}/STAR_index"
        bwa_index               = "${ref_directory}/bwa_index/bwa_index"
        bowtie2_index           = "${ref_directory}/bowtie2_index/bowtie2_base"
        sprint_index            = "${ref_directory}/sprint_index/genome.fa"
        hisat2_index            = "${ref_directory}/hisat2_index/genome"

    }

  }

}

building index

baseDir=/your/path/to/PipeOne/
nextflow run ${baseDir}/s1_RNAseq.nf -profile docker --genome hg38 --prepare_ref
## Delete intermediate files
rm -rf work result