What kind of Nanocompore outputs should be used?

[apbiomol]

Dear Wouter,

I am interested in using Methplotlib for visualizing m6A RNA frequencies and probability output by nanocompore.

The Nanocompore SampComp function generated several files named "simulated_shift.tsv", "simulated_report.tsv" and so on. Which files should I provide as inputs for Methplotlib. Could you explain a little bit more details on how to use Methplotlib with nanocompore outputs? Thanks for your time.

Sincerely, Wonyong

[wdecoster]

Hi Wonyong,

I have to admit I am not entirely sure anymore which filename you should use, but I can tell you that the header contains GMM_anova_pvalue. I hope that helps to narrow it down. Methplotlib should recognize which input type you supply, so you don't have to do anything special to use it for nanocompore. Please let me know if it does not work as expected.

Wouter

[apbiomol]

Hello Wouter,

Thanks for your reply. After I changed column header "GMM_logit_pvalue" to "GMM_anova_pvalue", the program seems to work fine, but I encountered another problem, calling the following statement "Found 0 gene(s) in the region". I checked my input files, but I couldn't find any problem.

I wonder if you could find time for checking my toy datasets output from nanocompore (only for one gene) and my gtf annotation file (including the one gene). My command lines were as shown below. I attached two files, 1) nanocompore_output.tsv and 2) annotation.gtf.

methplotlib -m nanocompore_output.tsv
-n frequencies
-w chr1:1,240,373-1,246,127
-g annotation.gtf
--simplify

Thanks in advance for whatever help I can get.

Sincerely, Wonyong

On Mon, Aug 9, 2021 at 9:31 PM Wouter De Coster @.***> wrote:

Hi Wonyong,

I have to admit I am not entirely sure anymore which filename you should use, but I can tell you that the header contains GMM_anova_pvalue. I hope that helps to narrow it down. Methplotlib should recognize which input type you supply, so you don't have to do anything special to use it for nanocompore. Please let me know if it does not work as expected.

Wouter

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[wdecoster]

It should not be necessary to change column names I think. I don't see any files here, but you can probably email them to me directly rather than through GitHub. You can find my email address in my profile.

[apbiomol]

I just forwarded the previous mail to your university email account (University of Antwerp). Thanks for your help.