Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

DNase compatibility #37

Open
StevenWingett opened this issue Aug 13, 2020 · 2 comments
Open

DNase compatibility #37

StevenWingett opened this issue Aug 13, 2020 · 2 comments
Labels
potential enhancement Possible enhancement, but not a priority

Comments

@StevenWingett
Copy link
Owner

Make HiCUP compatible with DNAse protocols.
@StevenWingett StevenWingett added the potential enhancement Possible enhancement, but not a priority label Aug 13, 2020
@asaki1986
Copy link

Hi @StevenWingett

Has this option been incorporated into the command? Or is there any option to support the hic data with DnaseI protocol?

Junfeng

@StevenWingett
Copy link
Owner Author

Hi Junfeng,

I've not had the time to incorporate this feature. Your best option would be to map the data with hicup_mapper and then de-duplicate the data with hicup_deduplicator. You could then filter the resulting BAM file to remove di-tags separated by a distance (of say, less then 1kb).

I hope that helps.

Best,
Steven

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
potential enhancement Possible enhancement, but not a priority
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@StevenWingett @asaki1986