Skip to content

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

@giacomogrillo7

Description

@giacomogrillo7

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

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions