Changes between Version 62 and Version 63 of SOPs/chip_seq_peaks

Timestamp:

10/12/21 15:57:59 (3 years ago)

Author:

thiruvil

Comment:

--

SOPs/chip_seq_peaks

@@ -214 +214 @@
 [[https://elifesciences.org/articles/46314| Improved CUT&RUN chromatin profiling tools]] from the Hanikoff lab, the developers of CUT&RUN, outline a protocol,
 
-   * Mapping: bowtie2 can be used for aligning the reads with the following parameters
+   * Mapping: bowtie2 can be used for aligning the reads with the following parameters (for paired-end reads)
       * --local 
       * --very-sensitive-local
@@ -222 +222 @@
       * -X 700
 
-   * Calling peaks: MACS2 is suitable to call peaks
-
+   * Calling peaks: MACS2 callpeak is suitable to call peaks
+      * -t treatment file
+      * -c control file
+      * -f BEDPE or BAMPE
+      * -g hs or mm
+      * –p 1e-5
+      * --keep-dup all
+      * --nomodel and --extsize can be used after strand cross-correlation [see above]
+
+
+