revmap_count: Reverse map small RNAs to processed or unprocessed reads

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Reverse map small RNAs to processed or unprocessed reads

Description

Reverse map small RNAs to processed or unprocessed reads

Usage

revmap_count(
  fastas,
  knownMiRNAs,
  bpparam = NULL,
  verbose = FALSE,
  linkers = NULL,
  length_max = NULL,
  length_min = NULL,
  removedups = TRUE,
  overwrite = FALSE,
  make_index = TRUE
)

Arguments

fastas	path to FASTA files to reverse map.
knownMiRNAs	path to FASTA file containing annotated miRNA or other small RNA sequences.
bpparam	TRUE or FALSE (default).
verbose	print messages, TRUE or FALSE (default).
linkers	contaminating sequences to remove, default is NULL, set to character string to specify.
length_max	maximum length required during fasta processing, default is NULL, set to integer to specify.
length_min	minimum length required during fasta processing, default is NULL, set to integer to specify.
removedups	remove multiple miRNAs or 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).
make_index	make bowtie2 index of reads, TRUE (default) or FALSE. If set to FALSE, indices should be in the same directory as reads.

Value

path to BEDs where small RNAs mapped to reads.

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)
testMiRNA <- system.file("extdata/hsa_mature.fa",package="CLIPflexR")
revmap <- revmap_count(FaFile_clip, testMiRNA, 
linkers="GGACGATGC", length_min=18, length_max=30, overwrite=TRUE)

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