Update IGV.md

Tuesday/IGV.md

@@ -54,7 +54,7 @@ You can access the Online help by clicking on “Help” in the bar menu then on
 
 - Load your own genome: in the bar menu, click on “Genomes” then on “Load genome from File”. Your genome should be an indexed FASTA file (.fa or .fasta)
 
-- You can also load a genome from an URL or a server.
+- You can also load a genome from an URL or a server, click on Genomes > Select Hosted Genomes .
         
         Ex: Mouse genome mm9 (showing all chromosomes by default)
 
@@ -123,12 +123,16 @@ The whole chromosome is shown by default. You can specify a genomic range (chr10
 
 - Possibility to load different types of data on the same reference genome
 - Load data from different locations (local, URL or server):
-    - From your computer : click on “File” > “Load From File” (previously saved from Galaxy using the floppy disk icon in a dataset)
+    - From your computer : click on “File” > “Load From File” 
     - From an Url: click on “File” > “Load From URL”
+    - From ENCODE: click on “File” > “Load From ENCODE (2012)” (available for hg19 and mm9)
+        - pick MEF signal and peaks
+        <img src="IGV_images/IGV_ENCODE.png" width="400">
+        
 
-### Save alignments from visible locus
-
-- Right-click on each alignment track then on “Export Alignments” to save visible alignments from the selected track in “.SAM” format
+        - Visualize actif gene (ex chr19:9,061,080-9,156,156 or Ahnak)
+        <img src="IGV_images/IGV_encodeView.png" width="800">
+    
 
 ### Saving your session
 
@@ -148,7 +152,7 @@ Warning: Data files must stay at the same location
 
 ### visualize ePeak session
 
-- Open the IGV_session in 12-IGV directory.
+- Open the igv_session.xml in 12-IGV directory.
 - Explore the data