-
Notifications
You must be signed in to change notification settings - Fork 3
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
Support for DNA methylation signal #8
Comments
Hello, This is something that is straightforward to implement given we already have methylation current level tables in f5c, yet, haven't found time to really implement it. Given that you asked now, I can get into implementing this sometime in the coming months. |
Great! Looking forward to it! Thanks. |
Hi, I am looking forward to it as well! |
Implementing support for this new RNA004 kit to squigulator. Will do the methylation as soon as that is finished. |
@HLHsieh and @xies4 You need to create a 3-column tsv file to have the chr, 0-based position and methylation frequency. For example:
Note that they must be tab separated. This example file is in test/methfreq.tsv If you have a f5c/nanopolish methylation frequency TSV, you can use the following command to generate the necessary file for squigulator:
Then you can provide this file to squigulator like below:
I tested this generated BLOW5 by basecalling (using buttery-eel) and running f5c:
The frequencies in afreq.tsv quite matched the ones in test/methfreq.tsv. |
Thank you @hasindu2008 |
Thank you for developing this amazing tool. I am wondering if there is a way to simulate reads with DNA methylation signals. If not, do you have any plan to include the function in the near future? Thanks again.
The text was updated successfully, but these errors were encountered: