extract_read_data: Extract the read data from a fast5 file

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

Extract the read data from a fast5 file

Description

This function can deal with both multifast5 files and single fast5 files. It can handle files basecalled with standard or the flip flop model.

Usage

extract_read_data(file_path = NA, read_id_fast5_file = NA,
  plot_debug = FALSE, basecalled_with, basecall_group, multifast5, model,
  plotting_library)

Arguments

file_path	a character string [NA]. Path of the single fast5 file. Use it if the file to be read is a single fast file. If the file to be read is multifast5 file, then keep this parameter as NA. Also set multifast5 flag to FALSE
read_id_fast5_file	a list [NA]. A list of 'read_id' and 'fast5_file' path. Use this option when a read from a multifast5 file is to be read. In such a case, you should set file_path to NA, and set multifast5 flag to TRUE.
plot_debug	a logical [FALSE]. Should data for plotting debug info in the plots be computed
basecalled_with	a character string. Specify if the data is from 'albacore' or 'guppy'
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"
multifast5	a logical. Set it to TRUE if the file to be processed is multifast5. Set it to FALSE if the file to be processed is a single fast5 file
model	a string. Set to 'flipflop' if the basecalling model is flipflop. Set to 'standard' if the basecalling model is standard model.
plotting_library	a string

Value

a list

Examples

## Not run: 

extract_read_data(file_path = '/path/to/the/file',
                  read_id_fast5_file = NA,
                  plot_debug = F,
                  basecalled_with = 'albacore',
                  basecall_group = 'Basecall_1D_000',
                  multifast5 = TRUE,
                  model = 'standard',
                  plotting_library = 'rbokeh')

## End(Not run)

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