Changes between Version 21 and Version 22 of SOPs/chip_seq_peaks

Timestamp:

07/23/15 15:22:10 (10 years ago)

Author:

thiruvil

Comment:

--

SOPs/chip_seq_peaks

@@ -264 +264 @@
 
   * Method 1: Run IDR to identify reproducible peaks
-  * Method 2: Intersect bound regions (peaks)
+  * Method 2: Use MACS2 [[https://github.com/taoliu/MACS/wiki/Call-differential-binding-events | bdgdiff]].  bedGraph (.bdg) files are required.
+  * Method 3: Intersect bound regions (peaks)
     * This binary comparison asks simply, "Is each peak in sample A present in sample B (and vice versa)?" 
     * This ignores the enrichment/score of each peak and gives each non-peak a score of 0.
-  * Method 3: Compare affinity (number of mapped reads) across bound regions
+  * Method 4: Compare affinity (number of mapped reads) across bound regions
     * Filter out redundant reads from each BAM file with a command like 'samtools rmdup'.
     * Merge peaks of all samples (and make non-redundant):
@@ -274 +275 @@
     * intersectBed -bed -wb -abam Reads_1.noDups.bam -b Peaks.bed | cut -f13-15 | mergeBed -i stdin -n > Peak_counts.reads_1.bed
     * Modify counts per peak to account for differing numbers of mapped reads.
-  * Method 4: Use [[http://code.google.com/p/ngsplot/ | ngsplot]] to make stacked heatmaps of peaks for each sample
-
+  * Method 5: Use [[https://github.com/shenlab-sinai/ngsplot | ngsplot]] to make stacked heatmaps,and profiles, of peaks for each sample
+