ciriAS.Rd
This function executes the docker container docker4circ where CIRI_AS is installed
ciriAS( group = c("sudo", "docker"), scratch.folder, sam.file, ciri.file, genome.file, annotation.file = NA )
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 |
sam.file, | a character string indicating the path to the RNA-Seq alignment SAM/BAM file from BWA |
ciri.file, | string indicating the path to the list of circRNAs |
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) |
annotation.file, | a character string indicating the path to the GTF/GFF file reporting the reference gene annotations |
The function returns the list of alternative circRNAs internal structures