Open
Conversation
Added a new argument ("genome") for the maxATAC average, normalize, predict, benchmark, and prepare functions. This allows users to specify other genomes for e.g., preparation of mm10 ATAC-seq bigWig files and mm10 predictions.
Without this argument, the default behavior of the above functions is to use hg38 genome files for all activities, even when genome files from other builds are specified.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Issue: the default behavior of maxATAC functions is to use hg38 genome files for all activities regardless of genome file specification. For example,
maxatac preparewill use the hg38 chrom.sizes and blacklist files even if mm10 chrom.sizes and blacklist files are specified by the user.Solution: added a new argument ("genome") for the
maxATAC average,normalize,predict,benchmark, andpreparefunctions in parser.py, which defaults to specifying the hg38 genome. This will allow users to specify other genomes when using maxATAC. I successfully tested the argument for all of the above functions by specifying--genome mm10in my function call.