Changes between Version 63 and Version 64 of SOPs/chip_seq_peaks

Timestamp:

10/12/21 16:30:08 (3 years ago)

Author:

thiruvil

Comment:

--

SOPs/chip_seq_peaks

@@ -210 +210 @@
 Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is an alternative method to ChIP-Seq: it improves on lower input, i.e. number of cells needed, and reducing antibody cross-reactivity.  CUT&RUN data analysis is similar to a typical ChIP-Seq.  
 
-Sequencing depth of 3 to 5 million reads per sample should be sufficient, though depths of more than 15 million reads will increase duplication rates  [[https://www.cellsignal.com/learn-and-support/frequently-asked-questions/cut-and-run-faqs#a26 |  Cell Signal FAQ]].
-
-[[https://elifesciences.org/articles/46314| Improved CUT&RUN chromatin profiling tools]] from the Hanikoff lab, the developers of CUT&RUN, outline a protocol,
+On average, sequencing depths of 3 to 5 million reads per sample should be sufficient, though depths of more than 15 million reads will increase duplication rates  [[https://www.cellsignal.com/learn-and-support/frequently-asked-questions/cut-and-run-faqs#a26 |  Cell Signal FAQ]].  Similar to ChIP-Seq, higher coverage is needed for histone marks compared to TF.
+
+The following protocol is slightly modified from [[https://elifesciences.org/articles/46314| Improved CUT&RUN chromatin profiling tools]],
 
    * Mapping: bowtie2 can be used for aligning the reads with the following parameters (for paired-end reads)