Reverse map small RNAs to processed or unprocessed reads

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

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)