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

trim-low-abund defaults to a k-mer size of 32 #191

Closed
jeanzzhao opened this issue Jul 14, 2022 · 2 comments · Fixed by #218
Closed

trim-low-abund defaults to a k-mer size of 32 #191

jeanzzhao opened this issue Jul 14, 2022 · 2 comments · Fixed by #218

Comments

@jeanzzhao
Copy link

jeanzzhao commented Jul 14, 2022 •
edited
Loading

Not sure why kmer size = 32 not 31 in one of my genome-grist run log file grun.log under zyzhao@farm:~/assembly-loss/grist folder.
Screen Shot 2022-07-14 at 2 53 13 PM
@ctb ctb changed the title Kmer size 32 trim-low-abund defaults to a k-mer size of 32 Jul 15, 2022
@ctb
Copy link
Member

ctb commented Jul 15, 2022

thanks, @jeanzzhao ! this happens because we do not specify the k-mer size when we call trim-low-abund.py, and so it defaults to k=32. I'll fix it in a bit.

@ctb ctb mentioned this issue Sep 25, 2022
Merged
@ctb ctb closed this as completed in #218 Sep 25, 2022
@ctb
Copy link
Member

ctb commented Sep 25, 2022

Fixed by #218!

Note, this should have minimal effect on results unless you're doing spacegraphcats, per discussion in #197. No need to rerun things IMO.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

[MRG] fix trim-low-abund ksize to match analysis ksize dib-lab/genome-grist
2 participants
@ctb @jeanzzhao