Chimera process CLIP data

chimera_Process(
  bams,
  fastas = NULL,
  knownMiRNAs,
  genomeIndex,
  exclude = NULL,
  bpparam = NULL,
  verbose = FALSE,
  removedups = TRUE,
  overwrite = FALSE
)

Arguments

bams

path to BAM files mapped to the genome, unmapped reads will be extracted for chimera processing. This requires that you mapped your reads to the genome disallowing soft clipping. If you allowed soft clipping, use fasta param and set bams = NULL.

fastas

path to reads to process if you want to perform chimera analysis on all reads, i.e. if you mapped your reads to the genome allowing soft clipping, default is NULL.

knownMiRNAs

path to FASTA file containing annotated miRNA or other small RNA sequence. Known miRNAs will be prioritized and known miRNA names must be in the format "miR-", "let-", "bantam-", "iab-".

genomeIndex

path to genome index.

exclude

names of small RNAs to remove, default is NULL, can be set to character vector to specify; must match names in knownMiRNAs file.

bpparam

TRUE or FALSE (default).

verbose

print messages, TRUE or FALSE (default).

removedups

remove multiple small RNAs mapping to the same read, TRUE (default) or FALSE. If TRUE, known miRNAs will be prioritized and known miRNA names must be in the format "miR-", "let-", "bantam-", "iab-".

overwrite

overwrite existing output files, TRUE or FALSE (default).

Value

path to chimera output table.

Author

Kathryn Rozen-Gagnon

Examples

testFastq <- system.file("extdata/SRR1742056.fastq.gz",package="CLIPflexR")
FqFile <- decompress(testFastq,overwrite=TRUE)
FaFile <- fastx_qtoa(FqFile)
FaFile_clip <- fastx_clipper(FaFile, writelog=FALSE)
myGenome <- system.file("extdata/hg19Small.fa",package="CLIPflexR")
myIndex <- suppressWarnings(bowtie2_index(myGenome, overwrite = TRUE))
myBam <- suppressWarnings(bowtie_align(FaFile_clip,myIndex, overwrite=TRUE))
miRNAs <- system.file("extdata/hsa_mature.fa",package="CLIPflexR")
chimera_bed <- chimera_Process(myBam, knownMiRNAs= miRNAs, genomeIndex = myIndex, 
exclude="hsa-miR-19a-3p", overwrite=TRUE, fastas = NULL)