In ottomagnusson/fastqR: Package to Read and Manipulate fastq Format Sequence Files

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(fastqR)

Background

FastQ files are composed of entries consisting of 4 lines 1. ID line. Starts with an @ symbol. Sequence ID is anything after that. IDs should be unique 2. Sequence line - should be a string of G/A/T/C/N bases 3. Mid line - starts with a + and are generally ignored. 4. Quality line. Should be a string of characters the same length as the sequence.

An example of a fastq file contain 2 sequence records would be:

@1HWUSI-EAS460:44:661VRAAXX:2:1:15253:1153 GCCNGGCTATGCAAGCAGGCTGCAGTGTGGATATAGTCGT +1HWUSI-EAS460:44:661VRAAXX:2:1:15253:1153 ???#;ABAAAHHHHGHFGDHEG@GG@GDGGB>DDDGBDD= @2HWUSI-EAS460:44:661VRAAXX:2:1:17398:1153 CAGNGAATCCTTGAGGCACCTTCTCTTATAAAAACA +2HWUSI-EAS460:44:661VRAAXX:2:1:17398:1153 BBB#BFFFEFHHHHHDHHHHHHHHHHHHHHHHHHHH

read_fastq

read_fastq reads a .fq format file and returnsa tibble with one row per fastq entry where the columns are:

1. ID (the sequence ID from the first line, minus the @)
2. Bases (the bases from the second line)
3. Qualities (the quality string from the 4th line)
4. GC (the GC content of the bases)

head(read_fastq(system.file("good.fq", package = "fastqR")))

gc_content

Take in a vector of DNA sequence strings and return a vector of %GC values (what percentage of the bases are G or C).

gc_content("GAGAGCGGCTT")

decode_qualities

Converts a scalar string of quality values into a vector of Phred scores.

Phred score = ASCII value of letter - offset

decode_qualities("???#;ABAAAH")

ottomagnusson/fastqR documentation built on Dec. 22, 2021, 5:20 a.m.