CUT&RUNTools 2.0 is a major update of CUT&RUNTools (link), including a set of new features specially designed for CUT&RUN and CUT&Tag experiments. Both of the bulk and single-cell data can be processed, analyzed and interpreted using CUT&RUNTools 2.0.

Single-cell data analysis

• raw data processing in parallel
• quality assessment and visualization
• feature-by-cell matrix construction
• dimensionality reduction and clustering analysis
• cell-type-specific pseudo-bulk data analysis

Bulk data analysis update

• supporting spike-in sequence alignment and data normalization
• options of experiment for CUT&RUN or CUT&Tag data analysis
• flexiable option for fragments selections (>120bp)
• supporting different peak calling strategies
• new functions for peaks annotation
• compatiable with more computational platforms

Please refer to Installation Instructions.

To learn new features for CUT&RUNTools 2.0 on the bulk data analysis, please see New features.

Once the package is installed, see Data Example for examples.

See Usage Page about how to set up the pipeline and detailed usage.

See Directory Structure for basic structure of input and output folders.

To get started, please see Overview.

See Data Example for a most excellent starting point to get familiar with the tool.

See Usage Page about how to set up the pipeline and detailed usage.

See Directory Structure for basic structure of input and output folders.

The schematic view of the single-cell data processing module of CUT&RUNTools

1. MEME does not work (well discussed in issue 20, issue 15, issue 2)
   potential solution: re-install MEME with either command

conda create -n meme meme=5.0.5 python=3.7
conda activate meme

conda create -n meme python=3.6
conda activate meme
conda install ‘meme=5.0.2’ ‘icu=58.2’

Here are the new updates after first publication of CUT&RUNTools 2.0 (07/9/2021).
We are really appreciated that all the users who used this tool and gave the feedback, riased issues, fixed the bugs and pulled requests, with us together to make this tool better.

xx/xx/xxxx - working on script of input control support (bulk)
09/02/2021 - support different types of adaptor processing (bulk) [details]
08/26/2021 - A singularity definition file for installation on their HPC cluster, thanks to qiyubio
07/29/2021 - bugs fixed in spike-in normalization (bulk)
07/23/2021 - add the scripts for get cut profiles of single locus/whole genome [details]
07/21/2021 - bugs fixed

CUT&RUNTools 2.0: A pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis, Bioinformatics, 2021

CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis, Genome Biol, 2019

Please cite our paper if you used CUT&RUNTools 2.0 in your study PubMed. If you run into issues and would like to report them, you can use the "Issues" tab on the left hand side.
Alternatively, you can contact authors: fyu{at}broadinstitute.org or guo-cheng.yuan{at}mssm.edu .