Installation¶
Dependencies¶
Trimming¶
Alignment¶
Annotating peaks¶
FAQ¶
Single end reads?¶
In the current implementation, proatac only supports paired-end reads. There’s some support on Biostars that explains what one should do given single-end sequencing data.
I found a bug / error; what do I do?¶
Please let us know if you find any errors/inconsistencies in the documentation or code by filing a new GitHub Issue.
I ran proatac; now what do I do?¶
A non-exhaustive list of ideas / resources includes:
- Perform nucleosome calling with NucleoATAC
- Identify variable transcription factors using chromVAR
- Compare peaks called from proatac to existing datasets. CistromeDB is a particularly useful resource for this.
Author¶
The primary developer is Caleb Lareau in the Aryee Lab <http://aryeelab.org> and the Buenrostro Lab.
Citation¶
If you use proatac in your research, please cite our tool at the following URL:
http://aryeelab.org/mgatk
Bugs / Errors¶
Please let us know if you find any errors/inconsistencies in the documentation or code by filing a new GitHub Issue.
