adjust_exons_of_long_reads: Adjust internal exons of full-length RNA-seq reads by...

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

Adjust internal exons of full-length RNA-seq reads by majority vote

Description

Adjust internal exons of full-length RNA-seq reads by majority vote

Usage

adjust_exons_of_long_reads(long_reads, max_exon_diff = 10)

Arguments

long_reads	GRangesList object.
max_exon_diff	Positive integer.

Value

GRangesList object with the same order of elements and same mcols as the input object.

Details

The input GRangesList object is returned by the extend_long_reads_to_TSS_and_PAS() function.
5'- and 3'-borders of exons in long_reads are clustered by similarity (within max_exon_diff bp). Then the exon borders are changed to the median value of genomic coordinates observed within the cluster. This suppresses the "fuzziness" of subalignments which are often observed in full-length RNA-seq reads.

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