Open kwonej0617 opened 1 year ago
Hi @kwonej0617,
One of the files from zenodo (HEK293T-WT-0-rep2
) is corrupted. It will be great if you can try out the file below:
https://drive.google.com/file/d/1BPWX8x_tJR2BCsMM-fWvSjqqspgJKkZ4/view?usp=sharing
Thanks!
Best wishes, Yuk Kei
Hi @yuukiiwa.
Thank you for your reply. Actually, HEK293T-WT-0-rep2 is not the dataset I downloaded to run xPore in this run. Here are the files I downloaded. Could you please check if any of these files are also corrupted or have some problem? HEK293T-WT-rep1.tar.gz HEK293T-WT-rep2.tar.gz HEK293T-WT-rep3.tar.gz HEK293T-KO-rep1.tar.gz HEK293T-KO-rep2.tar.gz HEK293T-KO-rep3.tar.gz
Thanks!!
Hi @kwonej0617,
Sorry for the delayed reply! I have found out why you got the empty diffmod.table
as the KO datapreps have transcript versions while the WT datapreps don't have transcript versions. Here I am attaching the datapreps for WT, which have transcript versions:
https://drive.google.com/drive/folders/1wUZVtBPV8epxosuXtwiix5Hp6dPe-Z_U?usp=share_link
Thanks!
Best wishes, Yuk Kei
Hi @yuukiiwa
I really appreciate your reply! When I decompressed WT1.tar.gz file, it contains data.index, data.json (Usually, when I run xpore dataprep, I got four types of file - data.index, data.json, data.readcount, and eventalign.index). I think xpore diffmod requires those four files ready. Therefore, would it be okay to substitute data.index and data.json files with the updated file and use the same data.readcount and eventalign.index files from the previous xpore dataprep output of HEK293T-WT-rep1 ?
Thank you for your help!
Hi @kwonej0617,
The data.json
and data.index
files are sufficient for running xpore diffmod
.
Thanks!
Best wishes, Yuk Kei
Thank you for your reply @yuukiiwa ! In xPore paper, it was mentioned that nf-core/nanoseq was used to generate preprocessing data. I want to try to run nf-core from raw rast5. Could you please share your nextflow.confg and main.nf files?
Thank you so much for your help!
Hi @kwonej0617,
You will have to clone the nf-core/nanoseq
pipeline, which includes both the nextflow config
and main.nf
files:
git clone https://github.com/nf-core/nanoseq.git
You can use the test config for RNA modification detection as a reference for the parameters and the the test data repository as a reference of the input directory structure.
Please join nf-core's slack channel if you run into problems when running nanoseq
.
Thanks!
Best wishes, Yuk Kei
Dear @ploy-np and @yuukiiwa, @jonathangoeke,
I downloaded preprocessed data of HEK293T-WT/KO-rep1,2,3 from https://doi.org/10.5281/zenodo.4587661 and run xpore 2.1 with those files. However, I didn't get any sites in the output file, diffmod.table, and only the header was printed. Could you please check if I made a mistake? Also, please give me suggestions to generate the result. Thank you so much!
Here is the command line to run xPore diffmod.
onfig.yml file looks like the following.![image](https://user-images.githubusercontent.com/80375662/223298369-8f1110b2-6498-4f3c-a52a-64a13bd4fe08.png)
Here are the downloaded preprocessed files.![image](https://user-images.githubusercontent.com/80375662/223298690-914e693b-7293-42f1-8374-a3aaf04c8ede.png)