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zhongzhd / ont_m6a_detection

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Reference file type #1

Closed kwonej0617 closed 1 year ago

kwonej0617 commented 1 year ago

Hi, Thank you for providing scripts to run m6a detection tools. I am a little bit confused to choose a reference file between the reference "genome" and "transcriptome". Looking at m6A detection tools you provided in github, it says to use reference transcriptome. How would the result be different if I use a reference genome?

I am looking forward to hearing from you!

Thank you!

zhongzhd commented 1 year ago

there is no difference, but it is worth noting that some tools do not support the reference "genome".

kwonej0617 commented 1 year ago

Thank you @zhongzhd for your reply.

In the nanopolish documentation, when it mentions a reference, it says reference genome. However, I saw that in the documentation of some m6a detection tools, they used reference transcriptome. Did you use reference transcriptome for nanopolish step?

Also, I have a question about having --reverse_sequence truein the base-calling process. I am wondering if it is necessary to have the option when performing the base-calling using RNA sequencing data even though I specified flow cell and kit number. Because the flow cell and kit are separated depending on either DNA or RNA sequencing, I thought I didn't have to do so. However, for example, the base-calling command line in nanocompore documentation includes the option. However, your pre-processing script and if I remember correctly, xPore didn't specify it. image

Finally, could you please upload the transcriptome reference, bed, and gtf files you used when running m6A detection tools or could you please share the database you downloaded each file from? While I've been trying to run m6A tools, I've gotten error messages and I assumed that the information of those are not matched each other.

I am looking forward to hearing from you! Thank you so much!

zhongzhd commented 1 year ago

Firstly, I apologize for not being able to reply to you in a timely manner due to my recent busy schedule. In fact, we used reference transcriptome for nanopolish step. And for the basecalling step, you can just specify a basic configuration file, like "rna_r9.4.1_70bps_hac.cfg". For the reference files, i don't know what species you're testing for. And if you encounter a error message while running a tool, you can try searching for similar issue under the corresponding tool's github.