Changes between Version 78 and Version 79 of SOPs/chip_seq_peaks

Timestamp:

11/09/21 13:35:14 (3 years ago)

Author:

thiruvil

Comment:

--

SOPs/chip_seq_peaks

@@ -235 +235 @@
         * note: MACS2 default is 1, i.e. keep one tag; high duplication rates in CUT&RUN may be due to poor data quality, see [[https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1802-4 | CUT&RUNTools]]
       * --nomodel and --extsize can be used after strand cross-correlation [see above]
+        * note: for paired-end reads (using BAMPE), these parameters are ignored since MACS2 will pileup and compute the 'extsize'.
 
 Called peaks should be filtered based on FDR, e.g. -log,,10,,(FDR) > 10, and other metrics, e.g. fold enrichment.  If CUT&RUN samples had low coverage, e.g. less than ~3 million reads, [[https://github.com/FredHutch/SEACR|SEACR]] may be an alternative to MACS to call peaks.