Intersect library fragments and not alignment in multibamcov #72
Conversation
This file contains 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
|
Thanks for the contribution! As I understand it, the goal is to count the entire size of the fragment - is that correct? |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
I've added an option to multiBamCov which extends one read (R1, right now) for properly paired alignments to the size of ISIZE before the intersection with the bed file. This should, in principle, count intersection of library fragments in place of alignments. I thought this can be useful to have a proper count when dealing with ChIP/MeDIP experiments.
A similar option may be considered for genomecov when -bg option is enabled