How to get '.bed' file containing TAD position for input matrix?

[X-xiaoyeren]

Hi, I have read your wonderful manuscript on BMC Bioinformations and now I can get the output file successfully. The output contains information about changing-point which is the left boundary of TAD. I'm very curious about how to get TAD position with hierarchical level value, and I correctly infer the hierarchy of 50kb's TAD, ranging from bin1 to bin93, from the output file. The inference is consistent to the upper-triangle image from HiCKeyR.

I'm really curious about apply this inference through whole chromosome in parallel, or how to get the message containing complete TAD boundary cites and hierarchical level values.

Thus, could you please point out any possible indirect output in HiCKey or HiCKey R processing that I ignored? Or, could you please set some parameter or function that could give users a file containing complete TAD boundary cites and hierarchical level values?

Any reply will be helpful. Thanks a lot！

[YingruWuGit]

Hi,

Thank you for reaching out. I’m so glad someone is using HiCKey.

You mean a file that record the start and end sites of each TAD for every hierarchical level? I think it’s not difficult to generate it from the “_output”. I will add it to the output files.

I’d send you a note when I finish it. Hopefully in a few days. Thank you so much for your suggestions.

On Tue, Jan 4, 2022 at 09:20 laofoye-xiaoyeren @.***> wrote:

Hi, I have read your wonderful manuscript on BMC Bioinformations and now I can get the output file successfully. The output contains information about changing-point which is the left boundary of TAD. I'm very curious about how to get TAD position with hierarchical level value, and I correctly infer the hierarchy of 50kb's TAD, ranging from bin1 to bin93, from the output file. The inference is consistent to the upper-triangle image from HiCKeyR.

I'm really curious about apply this inference through whole chromosome in parallel, or how to get the message containing complete TAD boundary cites and hierarchical level values.

Thus, could you please point out any possible indirect output in HiCKey or HiCKey R processing that I ignored? Or, could you please set some parameter or function that could give users a file containing complete TAD boundary cites and hierarchical level values?

Any reply will be helpful. Thanks a lot！

— Reply to this email directly, view it on GitHub https://github.com/YingruWuGit/HiCKey/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOQ6LRQKRWLQHNPKLMLQRLDUUL62ZANCNFSM5LHR2LDQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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[YingruWuGit]

Hi,

I've updated the repositories. Now it automatically generates another file "_TADs.bed", which is a basic bed file. If there is any error or other problems please feel free to contact me. Thank you.

On Tue, Jan 4, 2022 at 11:53 AM Yingru Wu @.***> wrote:

Hi,

Thank you for reaching out. I’m so glad someone is using HiCKey.

You mean a file that record the start and end sites of each TAD for every hierarchical level? I think it’s not difficult to generate it from the “_output”. I will add it to the output files.

I’d send you a note when I finish it. Hopefully in a few days. Thank you so much for your suggestions.

On Tue, Jan 4, 2022 at 09:20 laofoye-xiaoyeren @.***> wrote:

Hi, I have read your wonderful manuscript on BMC Bioinformations and now I can get the output file successfully. The output contains information about changing-point which is the left boundary of TAD. I'm very curious about how to get TAD position with hierarchical level value, and I correctly infer the hierarchy of 50kb's TAD, ranging from bin1 to bin93, from the output file. The inference is consistent to the upper-triangle image from HiCKeyR.

I'm really curious about apply this inference through whole chromosome in parallel, or how to get the message containing complete TAD boundary cites and hierarchical level values.

Thus, could you please point out any possible indirect output in HiCKey or HiCKey R processing that I ignored? Or, could you please set some parameter or function that could give users a file containing complete TAD boundary cites and hierarchical level values?

Any reply will be helpful. Thanks a lot！

— Reply to this email directly, view it on GitHub https://github.com/YingruWuGit/HiCKey/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOQ6LRQKRWLQHNPKLMLQRLDUUL62ZANCNFSM5LHR2LDQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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[X-xiaoyeren]

Appreciate for receiving your reply !

I've used the newest HiCKeyR package and get the bed file. There can be more TAD regions in all hierarchical orders. And I've made the structure inference in two languages in the appendix.

Wish your opinion on it and discussion !

------------------ 原始邮件 ------------------ 发件人: "YingruWuGit/HiCKey" @.>; 发送时间: 2022年1月8日(星期六) 下午3:11 @.>; @.**@.>; 主题: Re: [YingruWuGit/HiCKey] How to get '.bed' file containing TAD position for input matrix? (Issue #1)

Hi,

I've updated the repositories. Now it automatically generates another file "_TADs.bed", which is a basic bed file. If there is any error or other problems please feel free to contact me. Thank you.

On Tue, Jan 4, 2022 at 11:53 AM Yingru Wu @.***> wrote:

> Hi, > > Thank you for reaching out. I’m so glad someone is using HiCKey. > > You mean a file that record the start and end sites of each TAD for every > hierarchical level? I think it’s not difficult to generate it from the > “_output”. I will add it to the output files. > > I’d send you a note when I finish it. Hopefully in a few days. Thank you > so much for your suggestions. > > > > On Tue, Jan 4, 2022 at 09:20 laofoye-xiaoyeren @.> > wrote: > >> Hi, I have read your wonderful manuscript on BMC Bioinformations and now >> I can get the output file successfully. The output contains information >> about changing-point which is the left boundary of TAD. I'm very curious >> about how to get TAD position with hierarchical level value, and I >> correctly infer the hierarchy of 50kb's TAD, ranging from bin1 to bin93, >> from the output file. The inference is consistent to the upper-triangle >> image from HiCKeyR. >> >> I'm really curious about apply this inference through whole chromosome in >> parallel, or how to get the message containing complete TAD boundary cites >> and hierarchical level values. >> >> Thus, could you please point out any possible indirect output in HiCKey >> or HiCKey R processing that I ignored? Or, could you please set some >> parameter or function that could give users a file containing complete TAD >> boundary cites and hierarchical level values? >> >> Any reply will be helpful. >> Thanks a lot！ >> >> — >> Reply to this email directly, view it on GitHub >> <https://github.com/YingruWuGit/HiCKey/issues/1&gt;, or unsubscribe >> <https://github.com/notifications/unsubscribe-auth/AOQ6LRQKRWLQHNPKLMLQRLDUUL62ZANCNFSM5LHR2LDQ&gt; >> . >> Triage notifications on the go with GitHub Mobile for iOS >> <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&amp;mt=8&amp;pt=524675&gt; >> or Android >> <https://play.google.com/store/apps/details?id=com.github.android&amp;referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub&gt;. >> >> You are receiving this because you are subscribed to this thread.Message >> ID: @.> >> > -- > Andrew Y. Wu >

-- Andrew Y. Wu

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[YingruWuGit]

i was wondering where is the appendix?

[X-xiaoyeren]

Well, I sent the last comment via email. Maybe you could check the binding email. I’ll find one of your email addresses and send you the files.

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[YingruWuGit]

I didn't find any appendix in the email. Maybe you can send to arantilwu@gmail.com

[YingruWuGit]

I updated the repositories. Hope that would help you.

On Tue, Jan 11, 2022 at 2:34 PM laofoye-xiaoyeren @.***> wrote:

Well, I sent the last comment via email. Maybe you could check the binding email. I’ll find one of your email addresses and send you the files.

发自我的iPhone

Message ID: @.***>

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