This is a feature we requested some time ago that we have now implemented and tested on our own. We have created an assay that combines Hi-C with whole genome bisulfite sequencing. As such, we expect and even prioritize chimeric reads, and do not want to penalize or discard them.
We would prefer for the official ENCODE pipeline this to be using your original repository as opposed to our fork with this small change, so we hope you accept our pull request.
brentp
commented
3 years ago
This is a feature we requested some time ago that we have now implemented and tested on our own. We have created an assay that combines Hi-C with whole genome bisulfite sequencing. As such, we expect and even prioritize chimeric reads, and do not want to penalize or discard them.
Our preprint (in need of updating) is here: https://www.biorxiv.org/content/10.1101/481283v1.article-info
The ENCODE branch of the Juicer pipeline calls bwameth (look at CPU/juicer.sh for example): https://github.com/aidenlab/juicer/tree/encode
We would prefer for the official ENCODE pipeline this to be using your original repository as opposed to our fork with this small change, so we hope you accept our pull request.