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Transcriptomic reads convertion

tx_reads.Rd

Assign aligned reads to their respective gene models and convert their positions into their corresponding transcriptomic coordinate system. It also stitches together paired-end aligned reads into a single sequence in which dots '.' separate Read1 and Read2 by their corresponding insert.

Usage

tx_reads(
  reads,
  geneAnnot,
  minReads = 50,
  withSeq = FALSE,
  verbose = TRUE,
  ignore.strand = FALSE,
  nCores = 1
)

Arguments

reads

GAlignments or GAlignmentPairs. Genomic alignments to be processed

geneAnnot

GRanges. Gene annotation as loaded by tx_load_bed()

minReads

integer. Minimum number of alignments required to overlap a gene

withSeq

logical. Set to TRUE if sequence should be preserved; 'reads' object should contain sequences.

verbose

logical. Set to FALSE to show less information.

ignore.strand

logical. Set to TRUE to allow alignments in a gene ignoring the strand of the alignment. False by default.

nCores

integer. Number of cores to run the function with. Multi-core capability not available in Windows OS.

Value

GRanges

Details

To retrieve unassigned alignments use the function tx_get_unassignedAlignments()