chimera_process: Chimera process CLIP data

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Chimera process CLIP data

Description

Chimera process CLIP data

Usage

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(s)

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)

kathrynrozengagnon/CLIPflexR documentation built on Dec. 8, 2022, 7:31 p.m.