Match and filter

Introduction to Bioconductor in R

Paula Andrea Martinez, PhD.

Data Scientist

Duplicate sequences

Biological sequence duplicates occur in nature
Amplification from the steps in library preparation (PCR)
Sequencing the sample more than once

Remove duplicates or at least mark them

Whole genome sequencing or exome sequencing

Mark duplicates using a threshold

RNA-seq and ChIP-seq

srduplicated

library(ShortRead)

# Counting duplicates TRUE is the number of duplicates
table(srduplicated(dfqsample))

FALSE  TRUE 
500   500

# Cleaning reads from duplicates x[fun(x)]
cleanReads <- mydReads[srduplicated(mydReads) == FALSE]

# Counting duplicates
table(srduplicated(cleanReads))

FALSE
500

Creating your own filters

srFilter to filter based on a condition x[fun(x)]

Filter example

library(ShortRead)

# Use a custom filter to remove reads from fqsample
# This filter to remove reads shorter than a min number of bases
readWidthCutOff <- srFilter(function(x) {width(x) >= minWidth}, 
                            name = "MinWidth")

minWidth <- 51

fqsample[readWidthCutOff(fqsample)]

nFilter

library(ShortRead)

# save your filter, .name is optional
myFilter <- nFilter(threshold = 10, .name = "cleanNFilter")

# use the filter at reading point    
filtered <- readFastq(dirPath = "data", 
                      pattern = ".fastq",
                       filter = myFilter)

# you will retrieve only those reads that have a maximum of 10 N's
filtered

idFilter and polynFilter

library(ShortRead)

#id filter example
myFilterID <- idFilter(regex = ":3:1")
# will return only those ids that contain the regular expression

# optional parameters are .name, fixed and exclude
# use the filter at reading point    
filtered <- readFastq(dirPath = "data", pattern = ".fastq",
                       filter = myFilterID)

# filter to remove poly-A regions
myFilterPolyA <- polynFilter(threshold = 10, nuc = c("A"))
# will return the sequences that have a maximun number of 10 consecutive A's

# use the filter for subsetting    
filtered[myFilterPolyA(filtered)]

Let's practice using filters!

Introduction to Bioconductor in R