explore_basecaller_and_fast5type: Explore a fast5 file to find parameters of the experiment

In adnaniazi/tailfindr: Poly(A) Tail Length Estimator for Oxford Nanopore RNA and DNA Reads

Explore a fast5 file to find parameters of the experiment

Description

This function finds if a read is:

• multifast5 or single fast5

• 1D read or not-1D

• basecalled with Albacore or Guppy

• basecalled using standard model or flipflop model

• DNA or RNA

Usage

explore_basecaller_and_fast5type(fast5file_path, basecall_group)

Arguments

fast5file_path	a character string. Path of a fast5file for determining parameter of the experiment.
basecall_group	a character string. Name of the level in the Fast5 file hierarchy from which to read the data e.g. "Basecall_1D_000"

Value

A list containing the all the relevant data:

• basecalled_with: 'albacore', 'guppy'

• read_is_1d: TRUE, FALSE

• model: 'standard', 'flipflop'

• fast5type: 'multifast5', 'single'

• experiment_type: 'dna', 'rna'

Examples

## Not run: 

lst <- explore_basecaller_and_fast5type('/path/to/fast5/file',
                                        basecall_group='Basecall_1D_000')

## End(Not run)

adnaniazi/tailfindr documentation built on March 23, 2024, 7:07 a.m.