wrapperCiri.Rd
This function calls sequentially the docker containers for FASTQC, BWA, and CIRI to predict the list of circRNAs starting from the raw RNA-Seq reads
wrapperCiri( group = c("sudo", "docker"), scratch.folder, data.folder, genome.file, seq.type = c("se", "pe"), sample.id, threads = 1, annotation.file = "", max.span = 2e+05, stringency.value = c("high", "low", "zero"), quality.threshold = 10 )
group, | a character string. Two options: |
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scratch.folder, | a character string indicating the scratch folder where docker container will be mounted |
data.folder, | a character string indicating where gzip fastq files are located |
genome.file, | a character string indicating the path to the Fasta file of the reference genomic sequence (it should be the same reference indexed for the BWA alignment) |
seq.type, | a character string indicating the type of reads to be trimmed. Two options: |
sample.id, | a character string indicating the unique id to be associated to the bam that will be created |
threads, | a number indicating the number of cores to be used from the application |
annotation.file, | a character string indicating the path to the GTF/GFF file reporting the reference gene annotations |
max.span, | an integer reporting the maximum spanning distance of a circRNA (default = 200000 bp) |
stringency.value, | the selected stringency level of the analysis. Three possible options are available: "high" (high stringency, default), in which CIRI2 only provides circRNAs supported by more than 2 distinct PCC signals; "low" (low stringency), CIRI2 only provides circRNAs supported by more than 2 junction reads; "zero", CIRI2 provides all circRNAs regardless junction read counts or PCC signals |
quality.threshold, | integer indicating the threshold for mapping quality of each segment of junction reads (default=10) |
The list of circRNAs predicted by CIRI starting from the raw RNA-Seq datasets
if (FALSE) { #retrieve the example data system("wget https://github.com/carlo-deintinis/circhunter/archive/master.zip") #retrieve the data of the indexed genome (chromosome 21 of hg38 human genome assembly) system("unzip master.zip") system("unzip ./circhunter-master/CircHunter/data/hg38.chr21.fa.zip") system("wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR582/001/SRR5824251/SRR5824251_1.fastq.gz") #retrieve the RNA-Seq data system("wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR582/001/SRR5824251/SRR5824251_2.fastq.gz") #retrieve the RNA-Seq data #running the wrapperCiri function wrapperCiri(group = "docker", scratch.folder="/data/scratch", data.folder=getwd(), genome.file="./circhunter-master/CircHunter/data/hg38.chr21.fa", seq.type = "pe", sample.id="test", threads = 1, max.span = 200000, stringency.value = "high", quality.threshold = 10) }