read_ribobam: Read a bam file containing Ribosomal Footprints

In zslastman/RiboStan: Estimates Isoform Specific RPF Footprint Densities

Read a bam file containing Ribosomal Footprints

Description

This function

Usage

read_ribobam(ribobam, which, strip_seqnames = TRUE)

Arguments

ribobam	String; full path to html report file.
which	Select which reads to include (e.g. those that overlap with start and stop positions)
strip_seqnames	whether the function should remove all text after the first '|', useful if aligning to gencode fastas# Defaults to TRUE

Details

This function reads in a bam file containing ribosomal footprints. It uses only reads without splice sites and reads which align to the positive strand, as it's designed to work on transcriptomic alignments.

Value

This function returns a granges object with the read names in the names slot and a metadata column denoting readlength.

Author(s)

Dermot Harnett, [e-mail]

See Also

get_cds_reads, get_readlens

zslastman/RiboStan documentation built on April 6, 2024, 1:35 p.m.