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.

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

HOMER number of peaks does not correspond to found MACS2 peaks #50

Closed
ktrns opened this issue Sep 30, 2019 · 5 comments
Closed

HOMER number of peaks does not correspond to found MACS2 peaks #50

ktrns opened this issue Sep 30, 2019 · 5 comments

Comments

@ktrns
Copy link

ktrns commented Sep 30, 2019

Hi again,

We found that the cumulative number of peaks in the HOMER plot in the MultiQC report does not correspond to the found number of peaks by MACS2. Is this expected, and if so why?

Many thanks in advance!
Katrin

@drpatelh
Copy link
Member

Hi @ktrns . How much is it off by?

Can you navigate to the peak folder for that sample:
cd results/bwa/mergedLibrary/macs/

and run the command below?
cut -f 8 <SAMPLE_ID>.mLb.clN_peaks.annotatePeaks.txt | cut -d ' ' -f 1 | sort | uniq -c

That should give you a breakdown of how many peaks per feature from the output file itself. Are you able to spot any discrepancies?

It may be because HOMER uses NA values for some peaks its unable to annotate...

@ktrns
Copy link
Author

ktrns commented Sep 30, 2019

The HOMER figure sums up to more peaks than were found by MACS. I will check what you suggested and let you know. Thanks!

@ktrns
Copy link
Author

ktrns commented Sep 30, 2019

Hi again. Macs called 245 peaks. Running the command above and counting the numbers together, I get 245! The MultiQC HOMER figure though, sums up to much more.

BUT I just found the numbers I am expecting based on your command, in the HOMER figure for another sample. So it looks as if the sample labels are swapped in the figure.

@drpatelh
Copy link
Member

drpatelh commented Oct 4, 2019

Hi @ktrns ! This is indeed a bug. Ill get to the bottom of it and it will be fixed in the next release (hopefully soon!). Thanks for reporting.

245 is an awfully low number of peaks? Did something go wrong with the sample/library prep?

@drpatelh
Copy link
Member

Fixed in #52

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

No branches or pull requests

2 participants