extend_long_reads_to_TSS_and_PAS: Adjust outer borders of full-length RNA-seq reads to the...

In Maxim-Ivanov/TranscriptomeReconstructoR: Data-driven Annotation of the Transcriptome

Adjust outer borders of full-length RNA-seq reads to the nearby TSS and PAS

Description

Adjust outer borders of full-length RNA-seq reads to the nearby TSS and PAS

Usage

extend_long_reads_to_TSS_and_PAS(
  grl,
  tss,
  pas,
  read_flanks_up = c(-100, 10),
  read_flanks_down = c(-50, 50),
  trunc_limit = 20,
  mode = "reads",
  verbose = isTRUE(mode == "reads")
)

Arguments

grl	GRangesList object.
tss, pas	GRanges objects.
read_flanks_up, read_flanks_down	Integer vectors of length 2.
trunc_limit	Positive integer.
mode	Character. Must be either "reads" (default) or "transcripts".
verbose	Logical.

Value

GRangesList object containing the adjusted exons + some extra mcols.

Details

If mode == "reads", then grl is expected to be full-length RNA-seq reads returned by load_BAM_files(mode = "long_read").
If mode == "transcripts", then grl is expected to be known transcripts returned by exonsBy(txdb, by = "tx") (where txdb is a GenomicFeatures object).
tss and pas are returned by call_TCs() on 5'- and 3'-tag sequencing data, respectively.
The function searches for called TSS within read_flanks_up bp around 5' ends of long reads (or known transcripts), and for PAS within read_flanks_down around their 3' ends.
When neighboring TSS/PAS are found, the long reads are extended towards their summits.
If multiple TSS or PAS are found within the search window, then the one with the highest score is chosen.
The long read may be truncated, if the TSS/PAS summit is located inside of its terminal exon (however truncation to a length smaller than trunc_limit bp is disallowed).

Maxim-Ivanov/TranscriptomeReconstructoR documentation built on Oct. 3, 2023, 11:19 p.m.