Changes between Version 80 and Version 81 of SOPs/chip_seq_peaks

Timestamp:

11/17/21 13:56:23 (3 years ago)

Author:

gbell

Comment:

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SOPs/chip_seq_peaks

@@ -237 +237 @@
         * 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.
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+Called peaks should be filtered the same way as one would do with ChIP-seq peaks.
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