-
Notifications
You must be signed in to change notification settings - Fork 7
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
Using multiple samples in modkit dmr #140
Comments
Hello @ArnavBharti, Funny you should ask, the modkit v0.2.5 will do just what you're thinking. You can use |
Hello Team, Could you please elaborate more on modkit v0.2.5, as i also have the same query that if i have multiple control samples and treatment samples(with same disease condition) and i have concatenated all the bam files and if i run dmr pair, is it advisable to follow this approach. It would be nice to have your insights on the same. |
Hi @ArnavBharti, I am having trouble inputting multiple replicates into modkit dmr pair, because the command is not allowing me to. Were you able to manage? Lance |
Have you upgraded the modkit program? It was throwing an error on my side too saying "error: the argument '-a <CONTROL_BED_METHYL>' cannot be used multiple times". I pulled the repo again and built it. It is running and finishing succesfully |
Hi @ArnavBharti, Thanks a lot. Pulling the repo manually again made it work. |
The sample I have is sequencing of same vector, one carrying disease and one not. The control is from 5 sources. And the treatment from 2. I used this command. It is showing the output |
Could you show me the command you're using? Sites will be considered "failed" when there isn't enough valid coverage in all of the samples. Maybe decrease the valid coverage requirement? |
I will try this |
@ArnavBharti there is currently a limitation that requires the number of |
Here is the linux build, I also pushed the branch |
@ArnavBharti any luck? |
[dmr, single-site] Don't require that there is an even number of samples. See merge request machine-learning/modkit!153
It is working without error |
I have 5 control samples and 2 treatment samples. I used dmr multi and got multiple bed files since it does pairwise dmr.
Is it viable to use 'samtools merge' to combine the bam files and run modkit dmr pair?
These are not biological replicates. They are different and I have bam files for each of them individually.
The text was updated successfully, but these errors were encountered: