Problems in mmgenome2 with own dataset

[khuch123]

Initially, the error was "Error in .Call2("new_input_filexp", filepath, PACKAGE = "XVector") :
cannot open file 'data/assembly.fa", then when the path was provided it gave the following error:

"Error: The assembly contains duplicate sequence names"

Please help at the earliest.

Regards

[KasperSkytte]

Hi!

Sorry I haven't seen your post until now. You must ensure you have no duplicate scaffold names in the assembly. They must be unique.

[khuch123]

Sorry that was my mistake, I rectified it now. But the only thing I am again struggling with is mmplot, it says loading required package: shiny, for long it shows this command. Also, where do we get these values from 7.2, 16.2, 25.2 etc? selection <- data.frame(cov_C13.11.25 = c(7.2, 16.2, 25.2, 23.3, 10.1), cov_C14.01.09 = c(47, 77, 52.8, 29.5, 22.1)) Please help at the earliest

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On Fri, Aug 24, 2018 at 5:54 PM Kasper Skytte Andersen < ***@***.***> wrote: Hi! Sorry I haven't seen your post until now. You must ensure you have no duplicate scaffold names in the assembly. They must be unique. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#11 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AjEH4O5Z2Mrg_2-Uc8I2TEkE4uLuh757ks5uT_CEgaJpZM4WBNGC> .

[KasperSkytte]

shiny is required, so it loads it. Have a look at the get started guide here. It's coverage values

[khuch123]

Yes sir, I understood that but how for these specific values, sorry for multiple posts.

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On Fri, Aug 24, 2018 at 6:48 PM Kasper Skytte Andersen < ***@***.***> wrote: shiny is required, so it loads it. Have a look at the get started guide here <https://kasperskytte.github.io/mmgenome2/articles/mmgenome2.html>. It's coverage values — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#11 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AjEH4GYlH9SKGVzVuIBeSF0S5D4WvOgBks5uT_09gaJpZM4WBNGC> .

[KasperSkytte]

You get the coordinates by using the locator feature to extract scaffolds of interest. I assume you got those values from the examples, so it's just that, example points.

[khuch123]

Thank you very much for the help. Thank you very much once again. Please be there to always help us. Much regards and wishes

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On Fri, Aug 24, 2018 at 7:10 PM Kasper Skytte Andersen < ***@***.***> wrote: You get the coordinates by using the locator feature to extract scaffolds of interest. I assume you got those values from the examples, so it's just that, example points. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#11 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AjEH4NSfe9kdxkmUsH1EEucgmNkQumpBks5uUAI2gaJpZM4WBNGC> .

[KasperSkytte]

You're welcome