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source("https://bioconductor.org/biocLite.R")
biocLite("BSgenome.Mmusculus.UCSC.mm10")  

setwd("~/BIO2/MBDseq_Mouse_Muscle_Tcell_JungHo")

library(BSgenome.Mmusculus.UCSC.mm10)

chrs <- names(Mmusculus)[1:21]

CGs <- lapply(chrs, function(x) start(matchPattern("CG", Mmusculus[[x]]))) 

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# counting RNA-seq reads
# similar results with htseq-count w/ "UNION"

featureCounts -T 35 -p -t exon -g rmsk_id -a L1.ERV1.ERVK.ERVL.MaLR.gtf -o featureCounts.results \
sample1.bam sample2.bam sample3.bam

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printf "\nINDEL.profiler\n\n   usage: ./INDEL.profiler.sh READs.fasta Amplicon.seq.fasta\n\n"

cat $1 | \
while read l; do
	printf " \n"
      read L
	echo $l $L | sed 's/ /\n/g' | cat - $2 | muscle -quiet | fasta_formatter | \
	while read c; do
		printf "\n"$c"\nDEL:\n"
	      read d;

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#source("https://bioconductor.org/biocLite.R")
#biocLite("org.Mm.eg.db")

library("DESeq2")
library("calibrate")
library("pcaExplorer")
library("ggplot2")
library("gplots")
library("ggrepel")
library("gage")

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#source("https://bioconductor.org/biocLite.R")
#biocLite("TCGAbiolinks")

library(TCGAbiolinks)
library(data.table)
library(dplyr)
library(DT)

############################################################
# Clinical data 

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# deepTools - command line
# Use "--outFileNameMatrix" option to export data set (data are already oriented by strand)
    
$ computeMatrix scale-regions -p 40 -S low/*.bw -R ~/00-NGS/SETDB1_TCGA/GSE40419/promoter.10kb.bed 
-o SETDB1.low.Matrix.gz --skipZeros -bs 50 
-a 1000 -b 1000 --regionBodyLength 5000 
-bl ~/00-NGS/SETDB1_TCGA/GSE40419/blackList_LINE.LTR 
--outFileNameMatrix SETDB1.low.Matrix.tab

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####################################################################
# Load a count data

countsTable <- read.csv("counts.csv",row.names=1, header=T)
head(countsTable)
dim(countsTable)

####################################################################
# run DESeq2

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computeMatrix scale-regions -S 2m*.bw 20m*.bw 28m*.bw -R repeatMasker_mm10/ERV1.bed -o Muscle.ERV1.matrix.gz --skipZeros -bs 10 -a 1000 -b 1000 --regionBodyLength 2000 -bl blackList_LINE.LTR

plotHeatmap --whatToShow 'heatmap and colorbar' -m Muscle.ERV1.matrix.gz -out test.Muscle.ERV1.Heatmap.png --samplesLabel 2m-1 2m-2 20m-1 20m-3 28m-1 28m-2 --heatmapHeight 10 --heatmapWidth 1.5 --xAxisLabel "" --regionsLabel "" --startLabel "s" --endLabel "e" --colorList 'white,black'

plotProfile -m  Muscle.LINE.bin500.matrix.gz -out Muscle.LINE.bin500.Heatmap.pdf --plotFileFormat pdf --plotHeight 8 --perGroup --averageType mean --colors black red blue --plotType se --startLabel "start" --endLabel "end" --regionsLabel ""

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1. Google 'GSE40419' (GEO accession number)

2. Look for 'BioProject' or 'SRA' ID (RJNA173917 or ERP001058)

3. Go to 'SRA Run Selector' 

4. Enter "RJNA173917" or "ERP001058" in the search.

5. Choose samples to download.

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library(DESeq2)
library(pcaExplorer)
library(ggplot2)
library(gplots)
library(ggrepel)
library(reshape2)

# set working directory
setwd('~/00-NGS/SETDB1_TCGA/GSE40419/')