file_loading_and_checking: Loading and checking DNA barcodes.

In comoto-pasteur-fr/DNABarcodeCompatibility: A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms

Loading and checking DNA barcodes.

Description

Loads the file containing DNA barcodes and analyze barcode content.

Usage

file_loading_and_checking(file)

Arguments

file	The input data file that contains 2 columns separated by a space or a tabulation, namely the sequence identifiers and corresponding DNA sequence.

Details

This function loads the DNA barcodes from the input file and checks barcodes for unicity (identifier and sequence), DNA content, and equal size. It also calculates the fraction of G and C relative to A and T, as referred to as "GC content", and it detects the presence of homopolymers of length >= 3.

Value

A dataframe containing sequence identifiers, nucleotide sequence, GC content, presence of homopolymers.

Examples

write.table(DNABarcodeCompatibility::IlluminaIndexesRaw,
txtfile <- tempfile(), row.names = FALSE, col.names = FALSE, quote=FALSE)
file_loading_and_checking(txtfile)

comoto-pasteur-fr/DNABarcodeCompatibility documentation built on Sept. 17, 2024, 3:28 p.m.