SnapATAC2: Single Nucleus Analysis Pipeline for ATAC-seq

SnapATAC is a software package for analyzing scATAC-seq datasets. Conventional assays to map regulatory elements via open chromatin analysis of primary tissues is hindered by sample heterogeneity. SnapATAC dissects cellular heterogeneity in an unbiased manner and map the trajectories of cellular states.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive 
[user@cn4199 ~]$ module load SnapATAC2
[+] Loading singularity  3.10.3  on cn4199
[+] Loading SnapATAC2 2.1.2  ...
Running the test scripts:
[user@cn4199 ~]$ python $SNAPATAC2_TESTS/
[user@cn4199 ~]$ python $SNAPATAC2_TESTS/
[user@cn4199 ~]$ python $SNAPATAC2_TESTS/
[user@cn4199 ~]$ python $SNAPATAC2_TESTS/
Importing the python module snapatac2:
[user@cn4199 ~]$ python
Python 3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:53)
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import snapatac2 as snap
>>> snap.__version__