Analysis

Background

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head data/Targets.txt

## CellType InputFile   OutputFile
## A    A_1.txt.gz  A_1.bam
## A    A_2.txt.gz  A_2.bam
## B    B_1.txt.gz  B_1.bam
## B    B_2.txt.gz  B_2.bam

library(edgeR)
library(limma)
library(Rsubread)

targets <- readTargets("data/Targets.txt")

targets

##   CellType  InputFile OutputFile
## 1        A A_1.txt.gz    A_1.bam
## 2        A A_2.txt.gz    A_2.bam
## 3        B B_1.txt.gz    B_1.bam
## 4        B B_2.txt.gz    B_2.bam

celltype <- factor(targets$CellType)
design <- model.matrix(~celltype)
celltype

## [1] A A B B
## Levels: A B

buildindex(basename="chr1",reference="data/hg19_chr1.fa")

align(index="chr1",readfile1=paste("data",targets$InputFile, sep = "/"),input_format="gzFASTQ",output_format="BAM",output_file=targets$OutputFile,unique=TRUE,indels=5)

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