Changes between Version 68 and Version 69 of SOPs/chip_seq_peaks

Timestamp:

10/18/21 13:04:30 (3 years ago)

Author:

gbell

Comment:

--

SOPs/chip_seq_peaks

@@ -213 +213 @@
 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 reduces antibody cross-reactivity.  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.  For other details, see the   [[https://www.cellsignal.com/learn-and-support/frequently-asked-questions/cut-and-run-faqs |  Cell Signaling Technology FAQ]].  Similar to ChIP-Seq, higher coverage is needed for histone marks compared to transcription factor binding sites.
 
-CUT&RUN data analysis is similar to a typical ChIP-Seq.  The following protocol is slightly modified from [[https://elifesciences.org/articles/46314| Improved CUT&RUN chromatin profiling tools]],
+CUT&RUN data analysis is similar to a typical ChIP-Seq.  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)