| 210 | | Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is an alternative protocol 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 typical ChIP-Seq. |
| 211 | | |
| 212 | | |
| | 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. |
| | 211 | |
| | 212 | 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]]. |
| | 213 | |
| | 214 | [[https://elifesciences.org/articles/46314| Improved CUT&RUN chromatin profiling tools]] from the Hanikoff lab, the developers of CUT&RUN, outline a protocol, |
| | 215 | |
| | 216 | * Mapping: bowtie2 can be used for aligning the reads with the following parameters |
| | 217 | * --local |
| | 218 | * --very-sensitive-local |
| | 219 | * --no-mixed |
| | 220 | * --no-discordant |
| | 221 | * -I 10 |
| | 222 | * -X 700 |
| | 223 | |
| | 224 | * Calling peaks: MACS2 is suitable to call peaks |
| | 225 | |
