## ---- eval=FALSE----------------------------------------------------------- # setwd('/media/Storage/Work/MinION/') ## ---- eval=FALSE----------------------------------------------------------- # download.file(url='ftp://ftp.sra.ebi.ac.uk/vol1/ERA375/ERA375987/oxfordnanopore_native/H566_30_min_inc.tar.gz', # destfile = 'typhi.rep1.tar.gz') # download.file(url='ftp://ftp.sra.ebi.ac.uk/vol1/ERA375/ERA375685/oxfordnanopore_native/H566_ON_inc.tar.gz', # destfile = 'typhi.rep2.tar.gz') # download.file(url='ftp://ftp.sra.ebi.ac.uk/vol1/ERA376/ERA376255/oxfordnanopore_native/raw_2_rabsch_R7.tar.gz', # destfile = 'typhi.rep3.tar.gz') ## ---- eval=FALSE----------------------------------------------------------- # files.1 <- untar('typhi.rep1.tar.gz', list = TRUE) # extract.1 <- grep(pattern = "/FMH.*\\.fast5", files.1) # untar('typhi.rep1.tar.gz', files = files.1[extract.1], tar='internal', exdir = 'typhi.rep1') ## ---- eval=FALSE----------------------------------------------------------- # files.2 <- untar('typhi.rep2.tar.gz', list = TRUE) # extract.2 <- grep(pattern = "/FMH.*\\.fast5", files.2) # untar('typhi.rep2.tar.gz', files = files.2[extract.2], tar='internal', exdir = 'typhi.rep2') ## ---- eval=FALSE----------------------------------------------------------- # untar('typhi.rep3.tar.gz', files = 'raw_2_rabsch_R7/data_by_channel/', exdir = 'typhi.rep3') ## ---- eval=FALSE----------------------------------------------------------- # fast5.1 <- list.files(path = "typhi.rep1", pattern = "*.fast5$", # full.names = TRUE, recursive = TRUE) # fast5.2 <- list.files(path = "typhi.rep2", pattern = "*.fast5$", # full.names = TRUE, recursive = TRUE) # fast5.3 <- list.files(path = "typhi.rep3", pattern = "*.fast5$", # full.names = TRUE, recursive = TRUE) ## ---- eval=FALSE----------------------------------------------------------- # library(IONiseR) # s.typhi.rep1 <- readFast5Summary(files = fast5.1) # s.typhi.rep2 <- readFast5Summary(files = fast5.2) # s.typhi.rep3 <- readFast5Summary(files = fast5.3) ## ---- eval=FALSE----------------------------------------------------------- # addPassFail <- function(summaryData) { # ## calculate the mean base quality score for 2D reads # meanBaseQuality <- alphabetScore(quality(fastq2D(summaryData))) / width(fastq2D(summaryData)) # ## any greater than 9 is a PASS, less than is FAIL # passFail <- ifelse(meanBaseQuality > 9, yes = TRUE, no = FALSE) # ## match the PASS/FAIL status with an id # passFail <- data.table(baseCalled(summaryData) %>% # filter(full_2D == TRUE, strand== "template") %>% # select(id), pass = passFail) # ## create FALSE vector for all fast5 files, including those with no 2D # tmp <- rep(FALSE, length(summaryData)) # ## use the id field to set PASS for appropriate reads # tmp[filter(passFail, pass==TRUE)[,id]] <- TRUE # ## update readInfo slot with extract column # summaryData@readInfo <- mutate(readInfo(summaryData), pass = tmp) # return(summaryData) # } # # s.typhi.rep1 <- addPassFail(s.typhi.rep1) # s.typhi.rep2 <- addPassFail(s.typhi.rep2) # s.typhi.rep3 <- addPassFail(s.typhi.rep3) ## ---- eval=FALSE----------------------------------------------------------- # save(s.typhi.rep1, file = "styphi.rep1.rda") # save(s.typhi.rep2, file = "styphi.rep2.rda") # save(s.typhi.rep3, file = "styphi.rep3.rda")