add IA results

Tuesday/ePeak_PeakCalling.md

@@ -71,9 +71,9 @@ snakemake --use-singularity --singularity-args "-B '/home'" --cores $N
 
 ### Look at MultiQC report
 
-<img src="PC_images/MACS2_narrow.png" width="700" align="center" >
+<img src="PC_images/MACS2_narrow.png" width="1000" align="center" >
 
-<img src="PC_images/MACS2_broad.png" width="700" align="center" >
+<img src="PC_images/MACS2_broad.png" width="1000" align="center" >
 
 
 
@@ -94,11 +94,11 @@ compute_idr:
 
 - H3K27ac IDR results
 
-<img src="PC_images/H3K27ac_Rep_IDR.png" width="700" align="center" >
+<img src="PC_images/H3K27ac_Rep_IDR.png" width="1000" align="center" >
 
 - Klf4 IDR results 
 
-<img src="PC_images/Klf4_Rep_IDR.png" width="700" align="center" >
+<img src="PC_images/Klf4_Rep_IDR.png" width="1000" align="center" >
 
 
 - Do we have reproducible peaks?
@@ -117,7 +117,7 @@ intersectionApproach:
 
 
 ```
-wc -l *IA.bed
+wc -l 08-ReproduciblePeaks/macs2_broad/*IA.bed
 ```
 
 ### Look at MultiQC report
@@ -125,12 +125,16 @@ wc -l *IA.bed
 
 - IDR results
 
-<img src="PC_images/IDR_metrics.png" width="700" align="center" >
+<img src="PC_images/IDR_metrics.png" width="1000" align="center" >
 
 - IA results
 
-
-
+| Sample    | Number of peaks    | 
+|-----------|--------------------|
+| H3K27ac_shCtrl |  34284  |
+| H3K27ac_shUbc9 |  33803  |
+| Klf4_shCtrl    |  10577  |
+| Klf4_shUbc9    |  24199  |
 
 
 - Get the number of peaks with IA