Changes between Version 66 and Version 67 of SOPs/chip_seq_peaks
- Timestamp:
- 10/14/21 09:45:59 (3 years ago)
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SOPs/chip_seq_peaks
v66 v67 1 '''Contents:''' 2 * [#chipseq ChIP-Seq] 3 * [#CUTnRUN CUT&RUN] 4 1 5 2 6 == Using ChIP-Seq to identify and/or quantify peaks (or other interesting enriched regions) == 3 7 4 === Basic Approach===8 === [=#chipseq Basic Approach] === 5 9 * [#map Step 1: Map reads] 6 10 * [#cca Step 2: Perform strand cross correlation analysis] … … 186 190 intersectBed -a mm9_1KbUpDownofTSS.bed -b peaks.bed -wa -wb >| 1KbUpDownofTSS_peaks.bed 187 191 }}} 188 189 192 190 193 === [=#compare Step 6: Compare binding across different samples] === … … 206 209 207 210 208 == CUT&RUN==211 == [=#CUTnRUN CUT&RUN] == 209 212 210 213 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 reducing 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 [[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.
