This function calls sequentially the docker containers for FASTQC, STAR, and STARChip to predict the list of circRNAs starting from the raw RNA-Seq reads

wrapperSTARChip(
  group = c("sudo", "docker"),
  scratch.folder,
  genome.folder,
  samples.folder,
  threads,
  chimSegmentMin,
  chimJunctionOverhangMin,
  reads.cutoff,
  min.subject.limit,
  do.splice,
  cpm.cutoff,
  subjectCPM.cutoff,
  annotation
)

Arguments

group,

a character string. Two options: sudo or docker, depending to which group the user belongs

scratch.folder,

a character string indicating the scratch folder where docker container will be mounted

genome.folder,

a character string indicating the folder where the indexed reference genome for STAR is located.

samples.folder,

the folder where are located all the subfolders of the samples processed with starChimeric

threads,

a number indicating the number of cores to be used from the application

chimSegmentMin,

is a positive integer indicating the minimal length of the overlap of a read to the chimeric element

chimJunctionOverhangMin,

is a positive integer indicating the minimum overhang for a chimeric junction

reads.cutoff,

Integer. Minimum number of reads crossing the circRNA backsplice required.

min.subject.limit,

Integer. Minimum number of individuals with readsCutoff reads required to carry forward a circRNA for analysis

do.splice,

true false. The splices within the circRNA be detected and reported. Linear splices are searched within each circRNA in each individual. Any linear splice with >= 60% of the read count of the cRNA is considered a splice within the circRNA. Two files are then created, .consensus with most common splice pattern, and .allvariants with all reported splice patterns.

cpm.cutoff,

Float. Reads counts are loaded into R and log2(CountsPerMillion) is calculated using the limma package. With cpmCutoff > 0, circRNAs with log2(CPM) below this value will be filtered from this analysis

subjectCPM.cutoff,

Integer. See above. This value is the lower limit for number of individuals required to have the circRNAs expressed at a value higher than cpmCutoff.

annotation,

true/false. circRNAs are provided with gene annotations

Value

1. Count matrices : raw cRNA backsplice counts: circRNA.cutoff[readthreshold]reads.[subjectthreshold]ind.countmatrix log2CPM of above: norm_log2_counts_circRNA.[readthreshold]reads.[subjectthreshold]ind.0cpm_0samples.txt Maximum Linear Splices at Circular Loci: rawdata/linear.[readthreshold]reads.[subjectthreshold]ind.sjmax 2. Info about each circRNA: Consensus Information about Internal Splicing: Circs[reads].[subjects].spliced.consensus Complete Gene Annotation: circRNA.[readthreshold]reads.[subjectthreshold]ind.annotated Consise Gene Annotation + Splice Type: circRNA.[readthreshold]reads.[subjectthreshold]ind.genes 3. Images: PCA plots: circRNA.[readthreshold]reads.[subjectthreshold]ind.0cpm_0samples_variance_PCA.pdf Heatmap: circRNA.[readthreshold]reads.[subjectthreshold]ind.heatmap.pdf

Examples

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 wrapperSTARChip function wrapperSTARChip(group = "docker", scratch.folder="/data/scratch", genome.folder="./circhunter-master/CircHunter/data/", samples.folder=getwd(), threads = 8, chimSegmentMin = 20, chimJunctionOverhangMin = 15, reads.cutoff = 5, min.subject.limit = 1, do.splice = FALSE, cpm.cutoff = 0, subjectCPM.cutoff = 0, annotation = FALSE) }