Changes between Version 69 and Version 70 of SOPs/chip_seq_peaks

Timestamp:

10/19/21 10:39:59 (3 years ago)

Author:

thiruvil

Comment:

--

SOPs/chip_seq_peaks

@@ -216 +216 @@
 
    * Mapping: bowtie2 can be used for aligning the reads with the following parameters (for paired-end reads)
-      * --local 
+      * --local (end-to-end read alignment not required)
       * --very-sensitive-local
-      * --no-mixed 
-      * --no-discordant
-      * -I 10 
-      * -X 700
-
-   * Calling peaks: MACS2 callpeak is suitable to call peaks
+      * concordant pairs only:
+        * --no-mixed 
+        * --no-discordant
+      * -I 10 (min fragment length)
+      * -X 700 (max fragment length)
+
+   * Calling peaks: MACS2 //callpeak// is suitable to call peaks
       * -t treatment file
       * -c control file