wenjie1991

source("https://github.com/wenjie1991/bioinfo/blob/master/R/scatterBar.R")
source("https://github.com/wenjie1991/bioinfo/blob/master/R/ucscCancer_extractor.R")

#=================================================
# read data 
#=================================================
# read_csv
suppressMessages(dat.CNV <- read.ucscCancer.dir("../../../UCSC_cancer/COADREAD/TCGA_COADREAD_gistic2-2015-02-24/"))
suppressMessages(dat.mRNA <- read.ucscCancer.dir("../../../UCSC_cancer/COADREAD/TCGA_COADREAD_exp_HiSeqV2-2015-02-24"))

wenjie1991

# Alignemnt
```
## input file
inputFastq1=../data/fastq/input_R1.fastq.gz    ## input file name
inputFastq2=../data/fastq/input_R2.fastq.gz    ## input file name

## Output 
mkdir -p ../tmp/bam   ## Output fold
mappedBam=../tmp/bam/output.mapped.bam