Введение в ShortRead

Введение в Bioconductor на R

Paula Andrea Martinez, PhD.

Data Scientist

Геномы растений

Arabidopsis thaliana — небольшое цветковое растение
Первое растение с расшифрованным геномом
Размер генома: 135 мегапар оснований (Мп.о.)

Arabidopsis thaliana

Компании в области секвенирования

¹ Dan Koboldt massgenomics.org

fastq и 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")

Выборка fastq

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)

Вы готовы!

Введение в Bioconductor на R