Skip to content
New issue

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

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

Already on GitHub? # to your account

Use "getBackgroundPeaks" and save bakgrounds as bedfiles rather than indexes #117

Open
giacomogrillo7 opened this issue Sep 17, 2024 · 0 comments

Comments

@giacomogrillo7
Copy link

Hi,
I am currently answering reviewers' comments on our paper https://www.biorxiv.org/content/10.1101/2021.02.16.431334v3.
In this study we used chromVAR to score the enrichment of transposable element subfamilies (instead of motifs) in bulk ATAC-seq data. To answer one of the reviewers' comments I need to assess and provide the number of elements overlapping accessible chromatin in my samples and those overlapping the background files. Is there a way to save the background files as bedfiles or to convert the indexes obtained using getBackgroundPeaks to actual genomic locations?
Many thanks in advance!
Giacomo

# for free to join this conversation on GitHub. Already have an account? # to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant