diff --git a/Tuesday/ePeak_PeakCalling.md b/Tuesday/ePeak_PeakCalling.md index 69901522b992d32f679de9113b086846e45be0bf..ddf45582c26dc7c97feb6c86fde514fea771e3b7 100644 --- a/Tuesday/ePeak_PeakCalling.md +++ b/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