Wgd events of multi-genomes

[ardy20]

Hello I am trying to use this tool. I was wondering to use it for the WGD of 3 or more different genomes and combine the graph of multiple genomes in one figure file?

[SunPengChuan]

Multiple ks peaks of different genomes are shown in one Figure, you should use the ’-kf‘ parameter of WGDI.

[ardy20]

Thanks. Could you please give an example command?

[SunPengChuan]

You can first use wgdi -kf example >total.conf, then, there will be a file ks_fit_result.csv in the current directory, revise the species of Ks peaks, and execute the command wgdi -kf total.conf.

[ardy20]

Ok. What the example would be? genome.cds.fasta

[SunPengChuan]

The example is at https://github.com/SunPengChuan/wgdi-example/tree/main/dotplot/all.conf. Demo video at https://www.bilibili.com/video/BV1qK4y1U7eK and https://www.bilibili.com/video/BV195411P7L1.

[ardy20]

Thanks Sunpeng I am going to try it soon. Unfortunately the videos cannot be played in higher quality as it needs bilibili account which I couldn't create from Australia. Unfortunately I don't know chinese language. Is there any guide on how to prepare input files such as gff and lens files? Could the videos be uploaded on YouTube. Regards Ardy

[SunPengChuan]

I will upload a copy to youtube soon

[ardy20]

Ok Thanks. If you share it with me I can upload it on your behalf.

[SunPengChuan]

email ？

[ardy20]

Google Drive and then send the link to me, if possible.

[SunPengChuan]

https://drive.google.com/drive/folders/1zUSVD1rotLa9tBG-hXc3P5Mpr7d4ViB9?usp=share_link

[ardy20]

Thanks SunPeng I need your consent to upload on Youtube.

[SunPengChuan]

You can upload it, and it's even better if you add the English dub.

[ardy20]

Here are the You tube links:

Part 1: https://youtu.be/k-S6FVcBIQw

Part 2: https://youtu.be/QiZYFYGclyE

[erika-r-moore]

Here are the You tube links:

Part 1: https://youtu.be/k-S6FVcBIQw

Part 2: https://youtu.be/QiZYFYGclyE

Is it possible to get CC on these videos? I am hoping to auto-translate the video to English, but most solutions require CC first!

[SunPengChuan]

Yes, you can do that. I hope you can also add links to some examples, such as Karyotype evolution and phase subgenomes.

[erika-r-moore]

Hello! I have added English subtitles to the YouTube videos. Please note that the subtitles were generated using AI, so they may be incomplete or inaccurate.

Here are the YouTube links with English subtitles: Part 1: https://youtu.be/5Y_YszXcTsE Part 2: https://youtu.be/7jIgFyP1Vvk