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Genomic Analyses Using Radseq: 1. Raw Data Manipulation

The document describes analyzing raw Illumina sequencing data from stickleback fish using R. It demonstrates uploading and inspecting the raw sequence data, performing pattern matching and subsetting to extract reads containing a specific sequence, cleaning reads by removing those containing N's, and trimming reads. It provides example code and outlines tasks for the student to practice working with ShortRead objects - including uploading data, subsetting based on barcodes and sequences, determining proportions of reads meeting criteria, and writing out filtered reads.

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Suany Quesada Calderon
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16 views7 pages

Genomic Analyses Using Radseq: 1. Raw Data Manipulation

The document describes analyzing raw Illumina sequencing data from stickleback fish using R. It demonstrates uploading and inspecting the raw sequence data, performing pattern matching and subsetting to extract reads containing a specific sequence, cleaning reads by removing those containing N's, and trimming reads. It provides example code and outlines tasks for the student to practice working with ShortRead objects - including uploading data, subsetting based on barcodes and sequences, determining proportions of reads meeting criteria, and writing out filtered reads.

Uploaded by

Suany Quesada Calderon
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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Evolution and genomics, Cesky Krumlov

Daniel Berner
2. February 2016

Genomic analyses using RADseq:


1. Raw data manipulation
Demo
Upload and inspection of a raw Illumina sequence data set
(stickleback RAD sequences from the Misty system, Canada,
unpublished; 100k subset from a single SE100 Illumina lane)
library(ShortRead)
# d<-readFastq(dirPath='C:/Users/daniel/Documents/science/teaching/cesky
# krumlov 2016/course.materials/R.files',
# pattern='illumina.SE100.fastq', withIds=T)
d

## class: ShortReadQ
## length: 100000 reads; width: 100 cycles

# Call the read IDs of the ShortRead object


id(d)[1:4] # just the first four elements

## A BStringSet instance of length 4


## width seq
## [1] 53 BS-DSFCONTROL03:312:C3...1101:1232:2073 1:Y:0:
## [2] 53 BS-DSFCONTROL03:312:C3...1101:1213:2079 1:Y:0:
## [3] 53 BS-DSFCONTROL03:312:C3...1101:1185:2091 1:Y:0:
## [4] 53 BS-DSFCONTROL03:312:C3...1101:1102:2093 1:Y:0:
# Call the sequences
sread(d)[1:5]

## A DNAStringSet instance of length 5


## width seq
## [1] 100 CTGAATGCAGGTCATTTTGGTN...CGGACGNNNTCCCTGCATCCT
## [2] 100 TAGCATGCAGGAAGTCCGTTGN...CAACTCNNNAAAATTTGCCAA
## [3] 100 GCGCCTGCAGGGCTTTATCCAG...GCTGCTGNNCAGATGTCCTCC
## [4] 100 AGGTATATGCACAAAATGAGAT...CAATCTTNNCAAGCAACAGCA
## [5] 100 NCACGTGCACCAAAAAAAGAGT...NNNNNNNNNNNNNNNNNNNNN

# ... and their qualities


quality(d)[1:5]

## class: FastqQuality
## quality:
## A BStringSet instance of length 5
## width seq
## [1] 100 ;;<;@@2<@2222;@<<><;=#...#####################
## [2] 100 <<<??@<@=222@@@???@??#...#####################
## [3] 100 <<<@@@2<@22<@@@@?@?@@@...#####################
## [4] 100 <<<>?26@=))9>?@@@@@?<?...#####################
## [5] 100 #07>@222:))2=>@?@<;9>=...#####################
Pattern matching, counting

grep("TATATATATATATATATATA", sread(d))

## [1] 6053 15441 82461 84384

match <- grep("TATATATATATATATATATA", sread(d))


length(match)

## [1] 4

Subsetting of ShortRead object

d.match <- d[match]


sread(d.match)

## A DNAStringSet instance of length 4


## width seq
## [1] 100 TAGCATGCAGGGAGGCCTGTGT...TATTTTACACACAACGACAGA
## [2] 100 CTAGGTGCAGGTACAGTGATCG...TGCCTGCTCCCGACCGGCTTC
## [3] 100 CTGATGCAGGACAGGTCCTCCC...ATATATATATATATATATATC
## [4] 100 TAATGTGCAGGAGTCTGTAGTC...TATATATATATATATATATAT
Cleaning a ShortRead object

d.clean <- clean(d) # remove all reads with >= 1 'N'


sread(d.clean)[1]

## A DNAStringSet instance of length 1


## width seq
## [1] 100 CCATGTTGCAGGTGTGAAGGCT...GGGGACACGCCGGCCGTTTGC

Trimming a ShortRead object

d.trim <- narrow(d.match, start = 1, end = 10) # either end or width


quality(d.trim)

## class: FastqQuality
## quality:
## A BStringSet instance of length 4
## width seq
## [1] 10 ==>A<224?2
## [2] 10 BBCDF224A2
## [3] 10 @@@FFADDA2
## [4] 10 CCCFF222C2
Write a ShortRead object out as fastq file

# writeFastq(d.clean,
# file='C:/Users/daniel/Documents/science/teaching/cesky
# krumlov
# 2016/course.materials/R.files/my.clean.reads.fastq')
Tasks
I Upload the stickleback data set illumina.SE100.fastq
I Inspect the ID, sequence and quality of the reads 1000 to 1002
I Generate a new object X containing the data from the reads
10001-20000
I Determine the proportion of X’s reads containing one or more
’N’, and eliminate them from X
I What proportion of the filtered X is derived from the
individual with barcode (first five bases) ’CGATA’ ?
I Derive the object Y from X, including only these specific
CGATA-reads. Confirm that this worked by inspecting the
reads
I What proportion of Y’s reads contains the correct restriction
enzyme overhang ’TGCAGG’ at the correct position (i.e.,
following the barcode)? Copy these reads to object Z
I Clip the barcodes from Z, then write Z out as a fastq file

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