Changes between Version 47 and Version 48 of SOPs/chip_seq_peaks

Timestamp:

06/21/19 15:19:06 (6 years ago)

Author:

gbell

Comment:

--

SOPs/chip_seq_peaks

@@ -294 +294 @@
     * mergeBed -i Peaks_all_redundant.bed > Peaks.bed 
     * Count reads in each sample that overlaps each peak
-    * intersectBed -bed -wb -abam Reads_1.noDups.bam -b Peaks.bed | cut -f13-15 | mergeBed -i stdin -n > Peak_counts.reads_1.bed
+    * intersectBed -bed -wb -abam Reads_1.noDups.bam -b Peaks.bed | cut -f13-15 | groupBy -i stdin -g 1-3 -c 1 -o count > Peak_counts.reads_1.bed
     * Modify counts per peak to account for differing numbers of mapped reads.
   * Method 5: Use [[https://github.com/shenlab-sinai/ngsplot | ngsplot]] to make stacked heatmaps,and profiles, of peaks for each sample