params <-
list(isSlides = "no")
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)
AsSlides <- TRUE
## ----setup2, include=FALSE,eval=FALSE,echo=FALSE------------------------------
## library(ShortRead)
## temp <- readFastq("~/Projects/Results/RNAseqPipeTest/FirstTest/FQs/ENCFF000CXH.fastq.gz")
##
## ~/Downloads/out.fq
## temp <- readFastq("~/Downloads/out.fq")
## tAlin <- temp[sample(1:length(temp),10000)]
## writeFastq(tAlin,"~/Downloads/sampledActin.fq.gz")
## BiocInstaller::biocLite("QuasR")
## myFile <- data.frame(FileName="data/sampled_ENCFF000CXH.fastq.gz",SampleName="ENCFF000CXH")
## library("BSgenome.Hsapiens.UCSC.hg19")
## tis <- BSgenome.Hsapiens.UCSC.hg19[["chr5"]]
## writeXStringSet(DNAStringSet(list(chr5=tis)),"chr5.fa")
## write.table(myFile,"samples.txt",sep="\t",row.names=FALSE,quote=FALSE)
## qAlign("samples.txt","chr5.fa")
## library(Rsamtools)
## Rsamtools::sortBam("data/sampled_ENCFF000CXH_29a7bd074f7.bam","Sorted_sampled_ENCFF000CXH")
## Rsamtools::indexBam("Sorted_sampled_ENCFF000CXH.bam")
## myCoverage <- coverage("Sorted_sampled_ENCFF000CXH.bam")
## export.bw(myCoverage,con = "Sorted_sampled_ENCFF000CXH.bw")
##
## Rsamtools::indexBam("~/Downloads/ENCFF846QSN.bam")
##
## myFile <- data.frame(FileName="~/Downloads/sampledActin.fq.gz",SampleName="ENCFF000CXH")
## library("BSgenome.Hsapiens.UCSC.hg19")
## tis <- BSgenome.Hsapiens.UCSC.hg19[["chr7"]]
## writeXStringSet(DNAStringSet(list(chr7=tis)),"chr7.fa")
## write.table(myFile,"samples.txt",sep="\t",row.names=FALSE,quote=FALSE)
## qAlign("samples.txt","chr7.fa",splicedAlignment = TRUE)
## library(Rsamtools)
## Rsamtools::sortBam("~/Downloads/sampledActin_29a70b5f1d3.bam","sampledActinSpliced")
## Rsamtools::indexBam("sampledActinSpliced.bam")
## myCoverage <- coverage("Sorted_sampled_ENCFF000CXH.bam")
## export.bw(myCoverage,con = "Sorted_sampled_ENCFF000CXH.bw")
##
## Rsamtools::indexBam("~/Downloads/ENCFF846QSN.bam")
##
## ----results='asis',include=TRUE,echo=FALSE-----------------------------------
if(params$isSlides == "yes"){
cat("
class: inverse, center, middle
# Alignment
---
"
)
}else{
cat("
# Alignment
---
"
)
}
## ----sum2wcww, echo=TRUE,eval=FALSE,include=TRUE------------------------------
## BiocManager::install('Rsubread')
## library(Rsubread)
## ----sum2wcwwa, echo=FALSE,eval=TRUE,include=FALSE----------------------------
suppressPackageStartupMessages(library(Rsubread))
## ----load11, echo=TRUE,eval=FALSE---------------------------------------------
## BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")
## library(BSgenome.Hsapiens.UCSC.hg38)
## ----load1, echo=FALSE,eval=TRUE----------------------------------------------
suppressPackageStartupMessages(library(BSgenome.Hsapiens.UCSC.hg38))
## ----bsgenomeffft, echo=TRUE,eval=FALSE---------------------------------------
## chr7hg38 <- BSgenome.Hsapiens.UCSC.hg38[["chr7"]]
## chr7hg38Set <- DNAStringSet(list(chr7=chr7hg38))
## writeXStringSet(chr7hg38Set,file="chr7.fa")
## ----sum2wcwssw, echo=TRUE,eval=FALSE,include=TRUE----------------------------
## buildindex("chr7","chr7.fa", memory=8000)
## ----sum2waacww, echo=TRUE,eval=FALSE,include=TRUE----------------------------
## align("chr7","data/sampledActin.fq.gz",
## output_format = "BAM",
## output_file = "data/Rsubread_NoSplicing_sampledActin.bam")
## ----loadq, echo=TRUE,eval=FALSE----------------------------------------------
##
## BiocManager::install("Rsamtools")
## library(Rsamtools)
## ----loadq1, echo=FALSE,eval=TRUE---------------------------------------------
suppressPackageStartupMessages(library(Rsamtools))
## ----sort, echo=TRUE,eval=TRUE------------------------------------------------
sortBam("data/Rsubread_NoSplicing_sampledActin.bam","SortedActB")
## ----index, echo=TRUE,eval=TRUE-----------------------------------------------
indexBam("SortedActB.bam")
## ----sum, echo=TRUE,eval=TRUE,collapse=TRUE-----------------------------------
quickBamFlagSummary("SortedActB.bam")
## ----sum2wkaacww, echo=TRUE,eval=FALSE,include=TRUE---------------------------
## subjunc("chr7","data/sampledActin.fq.gz",
## output_format = "BAM",
## output_file = "data/RsubreadsampledActin.bam")
## ----sum2wcaww, echo=TRUE,eval=T,include=TRUE---------------------------------
sortBam("data/RsubreadsampledActin.bam",
"SortedActBSpliced")
indexBam("SortedActBSpliced.bam")
## ----sum2, echo=TRUE,eval=TRUE,collapse=TRUE----------------------------------
quickBamFlagSummary("SortedActBSpliced.bam")
## ----sum2ww, echo=FALSE,eval=FALSE,collapse=TRUE,include=FALSE----------------
## temp <- scanBam("SortedActBSpliced.bam")
## reads <- temp[[1]]$qname[is.na(temp[[1]]$mapq)]
## temp2 <- readGAlignments("~/Downloads/out.bam",param=ScanBamParam(what=c("qname", "strand", "pos", "qwidth")))
## temp3 <- temp2[temp2@elementMetadata$qname %in% reads]
## export(temp3,"missing.bam")
##
##
## library(Rsubread)
## Rsubread::buildindex("chr7","chr7.fa",gappedIndex = FALSE,indexSplit = FALSE)
## Rsubread::subjunc("/Users/tcarroll/Projects/Software/Github/RUBioconductor_Introduction/r_course/presentations/slides/chr7","/Users/tcarroll/Projects/Software/Github/RUBioconductor_Introduction/r_course/data/sampledActin.fq.gz",output_format = "BAM",output_file = "/Users/tcarroll/Projects/Software/Github/RUBioconductor_Introduction/r_course/data/RsubreadsampledActin.bam")
##
## temp <- scanBam("data/RsubreadsampledActin.bam")
## reads <- temp[[1]]$qname[is.na(temp[[1]]$mapq)]
## temp2 <- readGAlignments("~/Downloads/out.bam",param=ScanBamParam(what=c("qname", "strand", "pos", "qwidth")))
## temp3 <- temp2[temp2@elementMetadata$qname %in% reads]
## export(temp3,"missingRsubread.bam")
##
## qAlign("sampleTable.txt","chr7.fa",splicedAlignment = TRUE,maxHits = 100)
##
## ----loadbw2, echo=TRUE,eval=FALSE--------------------------------------------
##
## BiocManager::install("Rbowtie2")
## library(Rbowtie2)
## ----loadbw2_, echo=FALSE,eval=TRUE-------------------------------------------
suppressPackageStartupMessages(library(Rbowtie2))
## ----sumww2wvvcdhywwss, echo=TRUE,eval=FALSE,include=TRUE,tidy=FALSE----------
## bowtie2_build(references="chr7.fa",
## bt2Index=file.path("chr7hg38"))
## ----sumww2zzzzwcwwsslkkass, echo=TRUE,eval=FALSE,include=TRUE,tidy=FALSE-----
## library(R.utils)
##
## gunzip("data/sampledActin.fq.gz")
## ----sumww2wxxcwwsslkkass, echo=TRUE,eval=FALSE,include=TRUE,tidy=FALSE-------
## bowtie2(bt2Index = "chr7hg38",
## samOutput = "sampledActin.sam",
## seq1 = "data/sampledActin.fq")
## ----sumww2zzwcwwsslkkass, echo=TRUE,eval=FALSE,include=TRUE,tidy=FALSE-------
## bamFile_Bowtie2 <- asBam("sampledActin.sam")
## bamFile_Bowtie2
## ----sumww2wcxxwwsslkkass, echo=TRUE,eval=FALSE,include=TRUE,tidy=FALSE-------
## sortBam(bamFile_Bowtie2,"SortedActBSpliced_bowtie")
## indexBam("SortedActBSpliced_bowtie.bam")
## ----load, echo=TRUE,eval=FALSE-----------------------------------------------
## BiocManager::install("QuasR")
## library(QuasR)
## ----load1q, echo=FALSE,eval=TRUE---------------------------------------------
suppressPackageStartupMessages(library(QuasR))
## ----sampleTable1, echo=TRUE,eval=FALSE---------------------------------------
## FileName <- "data/sampledActin.fq.gz"
## SampleName <- "sampledActin"
## sampleTable <- data.frame(FileName,SampleName)
## write.table(sampleTable,file="sampleTable.txt",sep="\t",quote=FALSE,row.names = FALSE)
## sampleTable
## ----sampleTable1s, echo=FALSE,eval=TRUE--------------------------------------
FileName <- "data/sampledActin.fq.gz"
SampleName <- "sampledActin"
data.frame(FileName,SampleName)
## ----bsgenome, echo=TRUE,eval=FALSE-------------------------------------------
## library(QuasR)
## qAlign("sampleTable.txt", "BSgenome.Hsapiens.UCSC.hg38")
## ----bsgenomek, echo=TRUE,eval=FALSE------------------------------------------
## qAlign("sampleTable.txt","chr7.fa")
## ----bsgenomeka, echo=TRUE,eval=FALSE-----------------------------------------
## qAlign("sampleTable.txt","chr7.fa", aligner="Rhisat2")