search

xie186 / ViewBS

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

Flank option in meth over region and meth one region #8

Closed aditi-2017 closed 7 years ago

aditi-2017 commented 7 years ago

Hello,

Is it possible to set flanking region by option "-flank" as 0 or 10 for meth over region or meth one region command ? Right now if I try to set it as 10 I get this error :

The flank region size should be able to divivied by 1000 with no remainder The flank region size should be able to divivied by length of bin with no remainder

How can I change the length of flanking region in the output ? I will appreciate your reply.

Thank you Aditi

readbio commented 7 years ago

Currently, minimum length of '-length' should be 1000 bps and should be able to divided by 1000 with no remainder. My understanding is that you don't want the methylation patterns on the flanking region. Could you tell me a little bit more about your required feature? Then I can see whether I need to add this feature or not.

aditi-2017 commented 7 years ago

Hello,

Thank you for your reply.

I want to show small single bp methylation differences in gene body exons that might cause changes in RNA splicing, if I try to just plot one gene body exon it adds 1000 bp upstream and downstream to it and the emphasis of that single basepair difference is lost.

In other scenario, I only want to show differential methylation only in the promoter region (emphasizing specific motifs), but with addition of downstream flanking region some of the genic region is always included and I will have to cut it out.

If there was an option to choose window for display in meth over one region option and no flanking region unless specified, it would be nice. I am still able to work around the current option, i was just wondering if the other way was available.

Thank you

Aditi

On Thu, Apr 13, 2017 at 9:52 AM, readbio notifications@github.com wrote:

Currently, minimum length of '-length' should be 1000 bps and should be able to divided by 1000 with no remainder. My understanding is that you don't want the methylation patterns on the flanking region. Could you tell me a little bit more about your required feature? Then I can see whether I need to add this feature or not.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/readbio/ViewBS/issues/8#issuecomment-293901496, or mute the thread https://github.com/notifications/unsubscribe-auth/AYsMxCTMwkRjnO3rn0R5w7B9386kjArgks5rviiUgaJpZM4M4Hfp .

readbio commented 7 years ago

I'll add the feature later. I'll let you know if I update the code. Thanks for your information.

readbio commented 7 years ago

I have update the codes. Now you can set the flanking region size for the subcommand MethOneRegion. Please let me know if you have further questions.

aditi-2017 commented 7 years ago

That's great ! Thank you !

Aditi On Wed, Apr 26, 2017 at 5:50 PM readbio notifications@github.com wrote:

I have update the codes. Now you can set the flanking region size for the subcommand MethOneRegion. Please let me know if you have further questions.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/readbio/ViewBS/issues/8#issuecomment-297551753, or mute the thread https://github.com/notifications/unsubscribe-auth/AYsMxJxhkfcWZhO8cXmUsTZhC_n5Asc-ks5rz7wmgaJpZM4M4Hfp .