Introducing ShortRead

Introduction to Bioconductor in R

Paula Andrea Martinez, PhD.

Data Scientist

Plant genomes

Arabidopsis thaliana is a small flowering plant
First plant to have its genome sequenced
Genome size 135 megabase pairs (Mbp)

Arabidopsis thaliana

Sequencing companies

¹ Dan Koboldt massgenomics.org

fastq vs fasta

fastq

@ unique sequence identifier

raw sequence string

+ optional id

quality encoding per sequence letter

fastq, fq

fasta

> unique sequence identifier

raw sequence string

fasta, fa, seq

fasta

library(ShortRead)
# read fasta
fasample <- readFasta(dirPath = "data/", pattern = "fasta")

# print fasample
print(fasample)

class: ShortRead
length: 500 reads; width: 50 cycles

# methods accessors
methods(class = "ShortRead")

# Write a ShortRead object
writeFasta(fasample, file = "data/sample.fasta")

fastq

library(ShortRead)
# read fastq
fqsample <- readFastq(dirPath = "data/", pattern = "fastq")

# print fqsample
fqsample

class: ShortReadQ
length: 500 reads; width: 50 cycles

# methods accessors
methods(class = "ShortReadQ")

# Write a ShortRead object
writeFastq(fqsample, file = "data/sample.fastq.gz")

fastq sample

library(ShortRead)

# set the seed to draw the same read sequences every time
set.seed(123)

# Subsample of 500 bases
sampler <- FastqSampler("data/SRR1971253.fastq", 500)

# save the yield of 500 read sequences
sample_small <- yield(sampler)

# Class ShortReadQ
class(sample_small)
# length 500 reads
length(sample_small)

You are ready!

Introduction to Bioconductor in R