wrapperSTARChip: Wrapper function for circRNAs prediction using STARChip

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

Wrapper function for circRNAs prediction using STARChip

Description

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

Usage

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

Author(s)

Nicola Licheri, nicola [dot] licheri [at] unito [dot] it, University of Turin, Italy

Examples

## Not run: 

    #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) 


## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.