Recent changes to Home

Home modified by Kelly

Kelly — Wed, 05 Jun 2013 18:01:52 -0000

--- v38
+++ v39
@@ -43,8 +43,8 @@
 
 Installation
   Arpeggio
-Arpeggio can be installed by copying the latest distribution of ArpeggioJava to a folder of choice (e.g. /raid1/software/Arpeggio/). The latest distribution can be downloaded from Sourceforge at:

-   Download ArpeggioJava
+Arpeggio can be installed by copying the latest distribution of Arpeggio to a folder of choice (e.g. /raid1/software/Arpeggio/). The latest distribution can be downloaded from Sourceforge at:

+   Download Arpeggio
 

^back to the top

 
@@ -235,18 +235,18 @@

 Download the data from the SRA, map it and build all autocorrelation profiles

 
- java -Xmx4g -server -jar /raid1/software/ArpeggioJava/dist/ArpeggioJava.jar arpeggioInput/input_data bda     >> arpeggiolog.txt 

+ java -Xmx4g -server -jar /raid1/software/Arpeggio/Arpeggio.jar arpeggioInput/input_data bda     >> arpeggiolog.txt 

 
 

 Once the autocorrelation profiles are calculated, the controls can be matched:

 
- java -Xmx4g -server -jar /raid1/software/ArpeggioJava/dist/ArpeggioJava.jar  arpeggioInput/input_data ctr  >> arpeggiolog.txt 

+ java -Xmx4g -server -jar /raid1/software/Arpeggio/Arpeggio.jar  arpeggioInput/input_data ctr  >> arpeggiolog.txt 

 
 Note: the Arpeggio profiles and matching controls in the paper were calculated using R code, so there may be slight numerical differences.
 

 Finally, arpeggio profiles can be computed:

 
- java -Xmx4g -server -jar /raid1/software/ArpeggioJava/dist/ArpeggioJava.jar  arpeggioInput/input_data arp  >> arpeggiolog.txt 

+ java -Xmx4g -server -jar /raid1/software/Arpeggio/Arpeggio.jar  arpeggioInput/input_data arp  >> arpeggiolog.txt 

 
 

^back to the top

Home modified by Francesco Strino

Francesco Strino — Mon, 03 Jun 2013 23:35:14 -0000

--- v37
+++ v38
@@ -235,18 +235,18 @@

 Download the data from the SRA, map it and build all autocorrelation profiles

 
- java -Xmx4g -server -cp /raid1/software/ArpeggioJava/dist/ArpeggioJava.jar  arpeggio.gui.DataFill /raid1/sra/input_data bda     >> arpeggiolog.txt 

+ java -Xmx4g -server -jar /raid1/software/ArpeggioJava/dist/ArpeggioJava.jar arpeggioInput/input_data bda     >> arpeggiolog.txt 

 
 

 Once the autocorrelation profiles are calculated, the controls can be matched:

 
- java -Xmx4g -server -cp /raid1/software/ArpeggioJava/dist/ArpeggioJava.jar  arpeggio.gui.DataFill arpeggioInput/input_data ctr  >> arpeggiolog.txt 

+ java -Xmx4g -server -jar /raid1/software/ArpeggioJava/dist/ArpeggioJava.jar  arpeggioInput/input_data ctr  >> arpeggiolog.txt 

 
 Note: the Arpeggio profiles and matching controls in the paper were calculated using R code, so there may be slight numerical differences.
 

 Finally, arpeggio profiles can be computed:

 
- java -Xmx4g -server -cp /raid1/software/ArpeggioJava/dist/ArpeggioJava.jar  arpeggio.gui.DataFill arpeggioInput/input_data arp  >> arpeggiolog.txt 

+ java -Xmx4g -server -jar /raid1/software/ArpeggioJava/dist/ArpeggioJava.jar  arpeggioInput/input_data arp  >> arpeggiolog.txt 

 
 

^back to the top

Home modified by Kelly

Kelly — Mon, 03 Jun 2013 21:46:32 -0000

--- v36
+++ v37
@@ -281,7 +281,7 @@
 
 

-To create the nucleosome plots (figure 1 from the paper) run the following code in R (set your working directory to the input_data directory) using setwd() in R.
+To create the nucleosome plots (figure 1 from the paper) run the following code in R (set your working directory to the input_data directory) using setwd() in R.  (note that if you provided your own alignment rather than mapping with Arpeggio you will need to fill out the BDA.flattened.reads field in the data.csv with the number of unique mapped reads in the sample) 
 
 Arpeggio = read.table("Arpeggio.prof.csv", 
         header=TRUE, sep=",",row.names=NULL)

Home modified by Fabio Parisi

Fabio Parisi — Mon, 03 Jun 2013 21:00:49 -0000

--- v35
+++ v36
@@ -108,16 +108,16 @@

 
  cd /raid1/software 

- wget http://sourceforge.net/projects/bowtie-bio/files/bowtie/0.12.9/bowtie-0.12.9-linux-x86_64.zip/download 

- mv download bowtie-0.12.9-linux-x86_64.zip 

- unzip bowtie-0.12.9-linux-x86_64.zip 

- rm bowtie-0.12.9-linux-x86_64.zip 

+ wget http://sourceforge.net/projects/bowtie-bio/files/bowtie/1.0.0/bowtie-1.0.0-linux-x86_64.zip/download 

+ mv download bowtie-1.0.0-linux-x86_64.zip 

+ unzip bowtie-1.0.0-linux-x86_64.zip 

+ rm bowtie-1.0.0-linux-x86_64.zip 

 
 

 In order to map sequenced reads to the reference genome, it is necessary to "build" the genomes. The human and mouse reference genomes can be built using the following commands on a terminal window: 


 
- cd /raid1/software/bowtie-0.12.9 

+ cd /raid1/software/bowtie-1.0.0 

  scripts/make_mm9.sh && rm *.fa 

  scripts/make_hg19.sh && rm *.fa 

 
@@ -194,11 +194,10 @@
   files.sam=/raid1/sra/data/sam

   files.tmp=/raid1/sra/data/tmp


-  bowtie=/raid1/software/bowtie-0.12.9/bowtie

+  bowtie=/raid1/software/bowtie-1.0.0/bowtie

   bowtie.opt=-n2 -k1 -m1 --best --strata --chunkmbs 512

-  bowtie.genome.mm9=/raid1/software/bowtie-0.12.9/mm9

-  bowtie.genome.hg19=/raid1/software/bowtie-0.12.9/hg19

-  bowtie.genome.d_melanogaster_fb5_22=/raid1/software/bowtie-0.12.9/d_melanogaster_fb5_22

+  bowtie.genome.mm9=/raid1/software/bowtie-1.0.0/mm9

+  bowtie.genome.hg19=/raid1/software/bowtie-1.0.0/hg19


    fastq-dump=/raid1/software/sratoolkit.2.2.2a/bin/fastq-dump

Home modified by Fabio Parisi

Fabio Parisi — Mon, 03 Jun 2013 20:58:07 -0000

--- v34
+++ v35
@@ -290,15 +290,15 @@
         header=TRUE, sep=",",row.names=NULL)
 

 runmean=function(x,n){
-   d1=length(x)
-   d2=n
-   y = matrix(NA,length(x),d2)    
-   for(i in 1:d2){
-       j = max(1,d2/2 - i + 1,na.rm=TRUE):min(d1,d1 + d2/2 - i,na.rm=TRUE)
-       k = max(1,i - d2/2 + 1,na.rm=TRUE):min(d1,d1 - d2/2 + i,na.rm=TRUE)
-       y[k,i] = as.double(x[j])
-   }
-   apply(y,1,mean,na.rm=TRUE)
+  d1=length(x)
+  d2=n
+  y = matrix(NA,length(x),d2)    
+  for(i in 1:d2){
+    j = max(1,d2/2 - i + 1,na.rm=TRUE):min(d1,d1 + d2/2 - i,na.rm=TRUE)
+    k = max(1,i - d2/2 + 1,na.rm=TRUE):min(d1,d1 - d2/2 + i,na.rm=TRUE)
+    y[k,i] = as.double(x[j])
+  }
+  apply(y,1,mean,na.rm=TRUE)
 }
 

 makePretty = function(arpeg){

Home modified by Kelly

Kelly — Mon, 03 Jun 2013 20:42:23 -0000

--- v33
+++ v34
@@ -288,6 +288,18 @@
         header=TRUE, sep=",",row.names=NULL)
 BDAannotation = read.table("data.csv", 
         header=TRUE, sep=",",row.names=NULL)
+

+runmean=function(x,n){
+   d1=length(x)
+   d2=n
+   y = matrix(NA,length(x),d2)    
+   for(i in 1:d2){
+       j = max(1,d2/2 - i + 1,na.rm=TRUE):min(d1,d1 + d2/2 - i,na.rm=TRUE)
+       k = max(1,i - d2/2 + 1,na.rm=TRUE):min(d1,d1 - d2/2 + i,na.rm=TRUE)
+       y[k,i] = as.double(x[j])
+   }
+   apply(y,1,mean,na.rm=TRUE)
+}
 

 makePretty = function(arpeg){
   Arpeg = Arpeg[
@@ -304,7 +316,7 @@
   return(Arpeg)
 }
 

-Arpeg=Arpeggio[,BDAannotation[,"experiment.name"]=="H3K36me3_CD4T_NULL_1_C"]
+Arpeg=Arpeggio[,"H3K36me3_CD4T_NULL_1_C"]
 readsExp=BDAannotation[
     BDAannotation[,"experiment.name"]=="H3K36me3_CD4T_NULL_1_C",
     "BDA.flattened.reads"]
@@ -325,7 +337,7 @@
 legend("topright", c("H3K36me3","H3K27me3", "H3K27Ac", "pRB"),     cex=1.5,fill=c("blue","green","black","red")
  )
 

-Arpeg=Arpeggio[,BDAannotation[,"experiment.name"]=="H3K27me3_c2c12_MT_1"]
+Arpeg=Arpeggio[,"H3K27me3_c2c12_MT_1"]
 readsExp=BDAannotation[
     BDAannotation[,"experiment.name"]=="H3K27me3_c2c12_MT_1",
     "BDA.flattened.reads"]
@@ -341,7 +353,7 @@
     col="green"
  )
 

-Arpeg=Arpeggio[,BDAannotation[,"experiment.name"]=="pRb_GroFib_NULL_2"]
+Arpeg=Arpeggio[,"pRb_GroFib_NULL_2"]
 readsExp=BDAannotation[
     BDAannotation[,"experiment.name"]=="pRb_GroFib_NULL_2",
     "BDA.flattened.reads"]
@@ -357,7 +369,7 @@
     col="red"
  )
 

-Arpeg=Arpeggio[,BDAannotation[,"experiment.name"]=="H3K27Ac_HESC_NULL_2"]
+Arpeg=Arpeggio[,"H3K27Ac_HESC_NULL_2"]
 readsExp=BDAannotation[
     BDAannotation[,"experiment.name"]=="H3K27Ac_HESC_NULL_2",
     "BDA.flattened.reads"]

Home modified by Fabio Parisi

Fabio Parisi — Mon, 03 Jun 2013 19:31:15 -0000

--- v32
+++ v33
@@ -322,37 +322,56 @@
     type="l",
     ylab = bquote(.("IP signal") ~ (frac(Reads~ChIP,Total~Reads~ChIP))^2 ~ .("/") ~ (frac(Reads~Control,Total~Reads~Control))^2 ),
     xlab = "Offset(bp)", col="blue", ylim=c(0, 0.002))
-legend("topright", c("H3K36me3","H3K27me3", "H3K27Ac", "pRB"),     cex=1.5,fill=c("blue","green","black","red"))
+legend("topright", c("H3K36me3","H3K27me3", "H3K27Ac", "pRB"),     cex=1.5,fill=c("blue","green","black","red")
+ )
 

 Arpeg=Arpeggio[,BDAannotation[,"experiment.name"]=="H3K27me3_c2c12_MT_1"]
-readsExp=BDAannotation[BDAannotation[,"experiment.name"]
-=="H3K27me3_c2c12_MT_1","BDA.flattened.reads"]
-readsCtrl=BDAannotation[BDAannotation[,"experiment.name"]
-=="DNAInput_c2c12_MT_5","BDA.flattened.reads"]
+readsExp=BDAannotation[
+    BDAannotation[,"experiment.name"]=="H3K27me3_c2c12_MT_1",
+    "BDA.flattened.reads"]
+readsCtrl=BDAannotation[
+    BDAannotation[,"experiment.name"]=="DNAInput_c2c12_MT_5",
+    "BDA.flattened.reads"]
 ratio = readsExp^2/readsCtrl^2
 Arpeg = Arpeg/ratio
 Arpeg = makePretty(Arpeg)
-lines((-length(Arpeg)/4):(length(Arpeg)*1/4),Arpeg[(length(Arpeg)/4):(length(Arpeg)*3/4)], col="green")
+lines(
+    (-length(Arpeg)/4):(length(Arpeg)*1/4),
+    Arpeg[(length(Arpeg)/4):(length(Arpeg)*3/4)],
+    col="green"
+ )
 

 Arpeg=Arpeggio[,BDAannotation[,"experiment.name"]=="pRb_GroFib_NULL_2"]
-readsExp=BDAannotation[BDAannotation[,"experiment.name"]
-=="pRb_GroFib_NULL_2","BDA.flattened.reads"]
-readsCtrl=BDAannotation[BDAannotation[,"experiment.name"]
-=="IgG_VCaP_NULL_6","BDA.flattened.reads"]
+readsExp=BDAannotation[
+    BDAannotation[,"experiment.name"]=="pRb_GroFib_NULL_2",
+    "BDA.flattened.reads"]
+readsCtrl=BDAannotation[
+    BDAannotation[,"experiment.name"]=="IgG_VCaP_NULL_6",
+    "BDA.flattened.reads"]
 ratio = readsExp^2/readsCtrl^2
 Arpeg = Arpeg/ratio
 Arpeg = makePretty(Arpeg)
-lines((-length(Arpeg)/4):(length(Arpeg)*1/4),Arpeg[(length(Arpeg)/4):(length(Arpeg)*3/4)], col="red")
+lines(
+    (-length(Arpeg)/4):(length(Arpeg)*1/4),
+    Arpeg[(length(Arpeg)/4):(length(Arpeg)*3/4)],
+    col="red"
+ )
 

 Arpeg=Arpeggio[,BDAannotation[,"experiment.name"]=="H3K27Ac_HESC_NULL_2"]
-readsExp=BDAannotation[BDAannotation[,"experiment.name"]
-=="H3K27Ac_HESC_NULL_2","BDA.flattened.reads"]
-readsCtrl=BDAannotation[BDAannotation[,"experiment.name"]
-=="IgG_MCF7_NULL_1","BDA.flattened.reads"]
+readsExp=BDAannotation[
+    BDAannotation[,"experiment.name"]=="H3K27Ac_HESC_NULL_2",
+    "BDA.flattened.reads"]
+readsCtrl=BDAannotation[
+    BDAannotation[,"experiment.name"]=="IgG_MCF7_NULL_1",
+    "BDA.flattened.reads"]
 ratio = readsExp^2/readsCtrl^2
 Arpeg = Arpeg/ratio
 Arpeg = makePretty(Arpeg)
-lines((-length(Arpeg)/4):(length(Arpeg)*1/4),Arpeg[(length(Arpeg)/4):(length(Arpeg)*3/4)], col="black")
+lines(
+    (-length(Arpeg)/4):(length(Arpeg)*1/4),
+    Arpeg[(length(Arpeg)/4):(length(Arpeg)*3/4)],
+    col="black"
+ )

Home modified by Fabio Parisi

Fabio Parisi — Mon, 03 Jun 2013 19:28:21 -0000

--- v31
+++ v32
@@ -293,7 +293,7 @@
   Arpeg = Arpeg[
     c((length(Arpeg)/2+1):length(Arpeg),
     1:(length(Arpeg)/2))]

-   #remove large spike
+  #remove large spike
   Arpeg[length(Arpeg)/2] = (Arpeg[length(Arpeg)/2-1]*2 - 
         Arpeg[length(Arpeg)/2-2])
   Arpeg[length(Arpeg)/2+2] = (Arpeg[length(Arpeg)/2+3]*2 -
@@ -305,19 +305,24 @@
 }
 

 Arpeg=Arpeggio[,BDAannotation[,"experiment.name"]=="H3K36me3_CD4T_NULL_1_C"]
-readsExp=BDAannotation[BDAannotation[,"experiment.name"]
-=="H3K36me3_CD4T_NULL_1_C","BDA.flattened.reads"]
-readsCtrl=BDAannotation[BDAannotation[,"experiment.name"]
-=="DNAInput_c2c12_MT_4","BDA.flattened.reads"]
+readsExp=BDAannotation[
+    BDAannotation[,"experiment.name"]=="H3K36me3_CD4T_NULL_1_C",
+    "BDA.flattened.reads"]
+readsCtrl=BDAannotation[
+    BDAannotation[,"experiment.name"]=="DNAInput_c2c12_MT_4",
+    "BDA.flattened.reads"]
 ratio = readsExp^2/readsCtrl^2
 Arpeg = Arpeg/ratio
 

 Arpeg = makePretty(Arpeg)
 par(mgp = c(1.4, 0.5, 0))
-plot((-length(Arpeg)/4):(length(Arpeg)*1/4),Arpeg[(length(Arpeg)/4):(length(Arpeg)*3/4)], type="l",
-       ylab = bquote(.("IP signal") ~ (frac(Reads~ChIP,Total~Reads~ChIP))^2 ~ .("/") ~ (frac(Reads~Control,Total~Reads~Control))^2 ),
-       xlab = "Offset(bp)", col="blue", ylim=c(0, 0.002))
-legend("topright", c("H3K36me3","H3K27me3", "H3K27Ac", "pRB"), cex=1.5,fill=c("blue","green","black","red"))
+plot(
+    (-length(Arpeg)/4):(length(Arpeg)*1/4),
+    Arpeg[(length(Arpeg)/4):(length(Arpeg)*3/4)],
+    type="l",
+    ylab = bquote(.("IP signal") ~ (frac(Reads~ChIP,Total~Reads~ChIP))^2 ~ .("/") ~ (frac(Reads~Control,Total~Reads~Control))^2 ),
+    xlab = "Offset(bp)", col="blue", ylim=c(0, 0.002))
+legend("topright", c("H3K36me3","H3K27me3", "H3K27Ac", "pRB"),     cex=1.5,fill=c("blue","green","black","red"))
 

 Arpeg=Arpeggio[,BDAannotation[,"experiment.name"]=="H3K27me3_c2c12_MT_1"]
 readsExp=BDAannotation[BDAannotation[,"experiment.name"]

Home modified by Fabio Parisi

Fabio Parisi — Mon, 03 Jun 2013 19:24:25 -0000

--- v30
+++ v31
@@ -284,17 +284,24 @@

 To create the nucleosome plots (figure 1 from the paper) run the following code in R (set your working directory to the input_data directory) using setwd() in R.
 
-Arpeggio = read.table("Arpeggio.prof.csv", header=TRUE, sep=",",row.names=NULL)
-BDAannotation = read.table("data.csv", header=TRUE, sep=",",row.names=NULL)
+Arpeggio = read.table("Arpeggio.prof.csv", 
+        header=TRUE, sep=",",row.names=NULL)
+BDAannotation = read.table("data.csv", 
+        header=TRUE, sep=",",row.names=NULL)
 

 makePretty = function(arpeg){
-   Arpeg = Arpeg[c((length(Arpeg)/2+1):length(Arpeg),1:(length(Arpeg)/2))]
+  Arpeg = Arpeg[
+    c((length(Arpeg)/2+1):length(Arpeg),
+    1:(length(Arpeg)/2))]

    #remove large spike
-   Arpeg[length(Arpeg)/2] = (Arpeg[length(Arpeg)/2-1]*2 - Arpeg[length(Arpeg)/2-2])
-   Arpeg[length(Arpeg)/2+2] = (Arpeg[length(Arpeg)/2+3]*2 - Arpeg[length(Arpeg)/2+4])
-   Arpeg[length(Arpeg)/2+1] = (Arpeg[length(Arpeg)/2] + Arpeg[length(Arpeg)/2+2])/2
-   Arpeg = runmean(Arpeg,31)
-   return(Arpeg)
+  Arpeg[length(Arpeg)/2] = (Arpeg[length(Arpeg)/2-1]*2 - 
+        Arpeg[length(Arpeg)/2-2])
+  Arpeg[length(Arpeg)/2+2] = (Arpeg[length(Arpeg)/2+3]*2 -
+        Arpeg[length(Arpeg)/2+4])
+  Arpeg[length(Arpeg)/2+1] = (Arpeg[length(Arpeg)/2] + 
+        Arpeg[length(Arpeg)/2+2])/2
+  Arpeg = runmean(Arpeg,31)
+  return(Arpeg)
 }
 

 Arpeg=Arpeggio[,BDAannotation[,"experiment.name"]=="H3K36me3_CD4T_NULL_1_C"]

Home modified by Fabio Parisi

Fabio Parisi — Mon, 03 Jun 2013 19:17:31 -0000

--- v29
+++ v30
@@ -283,7 +283,7 @@
 

 To create the nucleosome plots (figure 1 from the paper) run the following code in R (set your working directory to the input_data directory) using setwd() in R.
-
+
 Arpeggio = read.table("Arpeggio.prof.csv", header=TRUE, sep=",",row.names=NULL)
 BDAannotation = read.table("data.csv", header=TRUE, sep=",",row.names=NULL)
 

@@ -307,7 +307,7 @@
 

 Arpeg = makePretty(Arpeg)
 par(mgp = c(1.4, 0.5, 0))
-plot((-length(Arpeg)/4):(length(Arpeg)*1/4),Arpeg[(length(Arpeg)/4):(length(Arpeg)*3/4)], type="l",
+plot((-length(Arpeg)/4):(length(Arpeg)*1/4),Arpeg[(length(Arpeg)/4):(length(Arpeg)*3/4)], type="l",
        ylab = bquote(.("IP signal") ~ (frac(Reads~ChIP,Total~Reads~ChIP))^2 ~ .("/") ~ (frac(Reads~Control,Total~Reads~Control))^2 ),
        xlab = "Offset(bp)", col="blue", ylim=c(0, 0.002))
 legend("topright", c("H3K36me3","H3K27me3", "H3K27Ac", "pRB"), cex=1.5,fill=c("blue","green","black","red"))
@@ -320,7 +320,7 @@
 ratio = readsExp^2/readsCtrl^2
 Arpeg = Arpeg/ratio
 Arpeg = makePretty(Arpeg)
-lines((-length(Arpeg)/4):(length(Arpeg)*1/4),Arpeg[(length(Arpeg)/4):(length(Arpeg)*3/4)], col="green")
+lines((-length(Arpeg)/4):(length(Arpeg)*1/4),Arpeg[(length(Arpeg)/4):(length(Arpeg)*3/4)], col="green")
 

 Arpeg=Arpeggio[,BDAannotation[,"experiment.name"]=="pRb_GroFib_NULL_2"]
 readsExp=BDAannotation[BDAannotation[,"experiment.name"]
@@ -330,7 +330,7 @@
 ratio = readsExp^2/readsCtrl^2
 Arpeg = Arpeg/ratio
 Arpeg = makePretty(Arpeg)
-lines((-length(Arpeg)/4):(length(Arpeg)*1/4),Arpeg[(length(Arpeg)/4):(length(Arpeg)*3/4)], col="red")
+lines((-length(Arpeg)/4):(length(Arpeg)*1/4),Arpeg[(length(Arpeg)/4):(length(Arpeg)*3/4)], col="red")
 

 Arpeg=Arpeggio[,BDAannotation[,"experiment.name"]=="H3K27Ac_HESC_NULL_2"]
 readsExp=BDAannotation[BDAannotation[,"experiment.name"]
@@ -340,7 +340,7 @@
 ratio = readsExp^2/readsCtrl^2
 Arpeg = Arpeg/ratio
 Arpeg = makePretty(Arpeg)
-lines((-length(Arpeg)/4):(length(Arpeg)*1/4),Arpeg[(length(Arpeg)/4):(length(Arpeg)*3/4)], col="black")
+lines((-length(Arpeg)/4):(length(Arpeg)*1/4),Arpeg[(length(Arpeg)/4):(length(Arpeg)*3/4)], col="black")