ShortRead परिचय

R में Bioconductor परिचय

Paula Andrea Martinez, PhD.

Data Scientist

पौधों के जीनोम

Arabidopsis thaliana एक छोटा पुष्पीय पौधा है
जीनोम सिक्वेंस होने वाला पहला पौधा
जीनोम आकार 135 मेगाबेस पेयर्स (Mbp)

Arabidopsis thaliana

सीक्वेंसिंग कंपनियाँ

¹ Dan Koboldt massgenomics.org

fastq बनाम 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 सैंपल

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)

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R में Bioconductor परिचय