Changes between Version 48 and Version 49 of SOPs/chip_seq_peaks

Timestamp:

06/24/19 10:22:53 (6 years ago)

Author:

gbell

Comment:

--

SOPs/chip_seq_peaks

@@ -292 +292 @@
     * Filter out redundant reads from each BAM file with a command like 'samtools rmdup'.
     * Merge peaks of all samples (and make non-redundant):
-    * mergeBed -i Peaks_all_redundant.bed > Peaks.bed 
+      * 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 | groupBy -i stdin -g 1-3 -c 1 -o count > Peak_counts.reads_1.bed
+      * multiBamCov -bams *.sorted.bam -bed Merged_peaks.bed > Merged_peak_counts.reads_samples.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