Parameters

Warning

Those parameters would cover the setting from nextflow.config file .

Mandatory

Note

plz configure those options in nextflow.config or docker.config file .

Name Example/Default value Description
–reads ``./*{1,2}.fq.gz `` input raw paired reads
–designfile FALSE A txt file that stored experimental design information, plz see details from ``–designfile `` section above
–comparefile FALSE A txt file that stored experimental compare information, plz see details from --comparefil e section above

Configuration

(paths to references, softwares and special environments. Only need to be set at the first time you run the pipeline) .
Name Example/Default value Description
–genomefile path/to/refdi r/chr2.fa Path to Fasta reference(requ ired if not set in config file)
–gtffile/– bedfile/–an notationfile path/to/refdi r/hg38_gencode. txt Different annotation files from GENCODE database for annotating circRNAs. e.g. [gencode.v25.a nnotation.gtf] /[gencode.v25. annotation.bed ]/[hg38_genco de.txt]
–ciridir/– find_circdi r/–mapsdir/ /path/to/tool s/directory Home folder of ciri/find_cir c/mapsplice installed location
–genomebuild
'hg19'
‘GRCh38’, ‘hg10’ available
specific genome
build for

circplot

Optional

Name Default value Description
-profile standard Configuration profile to use. Available: standard, conda, docker, singularity, test
–singleEnd false specify that the reads are single ended
–selectTools 1 specify which tools should be use. 1 for circexplorer2, 2 for ciri, 3 for find_circ, 4 for mapsplice, 5 for segemehl, For example, you can set 1,2,3,4,5 for running five tools in the same time.
–skipDE false skip differential expression analysis
–outdir ./Result the output directory of the results
–mRNA path/to/genco de.rsem.fpkm_m6 Astatus_11_29.m at Path to the mRNA expression matrix. Only need to be set when you want to do the correlation.

Detailed instruction of parameters

  • --reads

    suffix of your raw reads file. For example, *_{1,2}.fq.gz for paired end reads file sampleA_1.fq.gz and sampleA_2.fq.gz

  • --outdir

    path to the result output directory

  • --selectTools

    specify which tools should be use. 1 for circexplorer2, 2 for ciri, 3 for find_circ, 4 for mapsplice, 5 for segemehl. For example, you can set --selectTools='1,2,3,4,5' for running five tools in the same time.

  • --designfile

    design file

  • --comparefile

    compare file

  • --mRNA

    mRNA expression matrix file

  • --gtffile

    gtf file for building your STAR index, running CIRI and Mapsplice, running annotation. For example, gencode.v25.annotation.gtf.

  • --genomefile

    whole genome reference sequence in .fa format for running CIRCexplorer2, CIRI, Segemehl, Find_circ. For example, genome.fa.

  • --annotationfile

    annotation file of genome in .txt format for running CIRCexplorer2. For example, hg38_gencode.txt.

  • --singleEnd

    true when using a single End reads input, default false

Configure profiles

As a nextflow-based analysis pipeline, CircPipe allow users to edit configure file nextflow.config to set the index files and default file path parameters instead of typing them into the command line.

To configure, please go to params line, and set the following information of various file locations and system environment settings. Here, we use the test.config as an example.

  params {

//reads files
reads = "Fastq/*_{1,2}.fq.gz"

// design files and compare file
designfile="design.file"
comparefile="compare.txt"

currentPath="/data2/zhaoqi/circlePipetest/"
//the necessary reference
refmapsplice = false
annotationfile = "${currentPath}Genome/hg19_chr2_refseq.txt" // for using circexplorer2, can be obtained from
genomefile = "${currentPath}Genome/hg19_chr2.fa"
faifile = "${currentPath}Genome/hg19_chr2.fa.fai"
gtffile = "${currentPath}Genome/hg19_chr2.gencode.annotation.gtf"
mRNA = ""

// index files for each software
starindex = "${currentPath}Genome/hg19_chr2_starindex"// path and prefix
segindex = "${currentPath}Genome/hg19_chr2" // path only
hisat2_index = "${currentPath}Genome/hg19_chr2_hisat2_index/hg19_chr2"
bowtie2index = "${currentPath}Genome/hg19_chr2" // path and prefix
bowtieindex = "${currentPath}Genome/hg19_chr2" // path and prefix
bwaindex = "${currentPath}Genome/hg19_chr2" //path and prefix
skipDE = false

}