search

xie186 / ViewBS

ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data
GNU General Public License v3.0
81 stars 27 forks source link

Problem with MethGeno plots #54

Closed RubioB closed 3 years ago

RubioB commented 3 years ago

Hi,

I am new to using ViewBS, so I have a problem with the MethGeno output. Indeed, I would have liked to be able to obtain, as in the tutorial, the levels of methylation by chromosomes, with an independent graph for each chromosome. However, at the output I get a single graph with the methylation levels on the y-axis and on the x-axis I have all the scaffolds while I should have the chromosome coordinates (?). I expected to have as many graphics as scaffolds. For information, I had launched a first analysis with the same command line of the tutorial but I had an error linked with the fact that I have a large number of scaffolds (1408). Is that what is causing a problem ? I have tried changing the parameters --maxChrNumber, --step, --win but without success...

Can you tell me what's going on ?

Thanks in advance !

B. Rubio

xie186 commented 3 years ago

Sorry for the late response. I'll look into this today and get back to you.

RubioB commented 3 years ago

Thank you for your reply !

Have you had time to look at my problem ?

De : Shaojun Xie notifications@github.com Envoyé : mardi 13 octobre 2020 14:14 À : xie186/ViewBS ViewBS@noreply.github.com Cc : RubioB bernadetterubio@hotmail.com; Author author@noreply.github.com Objet : Re: [xie186/ViewBS] Problem with MethGeno plots (#54)

Sorry for the late response. I'll look into this today and get back to you.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/xie186/ViewBS/issues/54#issuecomment-707767684, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AMV7LRYWHOV6CYXTKHBA7RDSKROCZANCNFSM4SI6QLYQ.

xie186 commented 3 years ago

Thank you for your reply ! Have you had time to look at my problem ? … ____ De : Shaojun Xie notifications@github.com Envoyé : mardi 13 octobre 2020 14:14 À : xie186/ViewBS ViewBS@noreply.github.com Cc : RubioB bernadetterubio@hotmail.com; Author author@noreply.github.com Objet : Re: [xie186/ViewBS] Problem with MethGeno plots (#54) Sorry for the late response. I'll look into this today and get back to you. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#54 (comment)>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AMV7LRYWHOV6CYXTKHBA7RDSKROCZANCNFSM4SI6QLYQ.

If you don't have scaffolds at chromosome level, I would not recommend you to use this function. If you have, I would recommend you to include the chromosome level scaffolds in the input file.

Best, Shaojun