find_dna_tailtype: Finds if a DNA read is poly(A) read or poly(T) read

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

Finds if a DNA read is poly(A) read or poly(T) read

Description

This function reads the data from a fast5 file, and then alings primers to the read to discover if it is a poly(A) or poly(T) read. For poly(A) reads, the function further tests if the read is a complete read – and not truncated prematurely. The function also find the rough end site of the poly(A) tail, and the rough start site of the poly(T) tail.

Usage

find_dna_tailtype(file_path = NA, basecall_group = "Basecall_1D_000",
  dna_datatype = "cdna", plot_debug = FALSE, basecalled_with,
  multifast5, model, read_id_fast5_file = NA, plotting_library, ...)

Arguments

file_path	a character string[NA]. Full path of the read whose type is to be determined. Use it if the read is basecalled with Albacore and is of one-read-per-fast5 type.
dna_datatype	a character string ['cdna']. Specify if the read is 'cdna' or pcr-dna'.
plot_debug	a logical [FALSE]. Specifies whether to compute data needed for plotting debug.
basecalled_with	a character string. Specify if the data is from 'albacore' or 'guppy'
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.l
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.
plotting_library	a string.
...	An other parameter. For future expansion.

Value

A list containing all the relevant information

Examples

## Not run: 

# 1. If the data is multifast5 cDNA (direct cDNA or amplified cDNA)
data basecalled with flip-flop algorithm
read_id_fast5_file = list(read_id=read_id, fast5_file=full_path_of_fast5_file)
find_dna_tailtype(dna_datatype = 'cdna',
                  multifast5 = TRUE,
                  basecalled_with = 'guppy',
                  model = 'flipflop',
                  read_id_fast5_file = read_id_fast5_file)

# 2. If the data is multifast5 pcr-DNA data basecalled with flip-flop
algorithm
read_id_fast5_file = list(read_id=read_id, fast5_file=full_path_of_fast5_file)
find_dna_tailtype(dna_datatype = 'pcr-dna',
                  multifast5=TRUE,
                  basecalled_with = 'guppy',
                  model = 'flipflop',
                  read_id_fast5_file = read_id_fast5_file)

# 3. If the data is cDNA (direct cDNA or amplified cDNA) data basecalled with
albacore with single fast5 files as output
find_dna_tailtype(file_path = full_file_path_of_the_read,
                  dna_datatype = 'cdna',
                  multifast5 = FALSE,
                  basecalled_with = 'albacore',
                  model = 'standard')

## End(Not run)

adnaniazi/tailfinder documentation built on March 23, 2024, 5:41 p.m.