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Identification of chromatin loops using deep learning
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Why there are 22580 sequences in every directions in the IMR90 cell line #2

Open ZhangPY-bioinformatics opened 3 years ago

ZhangPY-bioinformatics commented 3 years ago

I'm sorry to disturb you, but I encountered something very puzzled while studying your paper. You mentioned in your paper that there are 22580 sequences in the IMR90 cell line, but in github, your IMR90 cell line has 22580 sequences in every directions. And in different directions, many sequences are repeated. Is my understanding wrong?

linDing-group commented 3 years ago

Hi, There must be misunderstanding. Since the same sequence would form a loop structure with other different sequences in different directions, so it is normal for a certain sequence to appear repeatedly.

------------------ 原始邮件 ------------------ 发件人: "linDing-group/Deep-loop" @.>; 发送时间: 2021年10月3日(星期天) 中午12:11 @.>; @.***>; 主题: [linDing-group/Deep-loop] Why there are 22580 sequences in every directions in the IMR90 cell line (#2)

I'm sorry to disturb you, but I encountered something very puzzled while studying your paper. You mentioned in your paper that there are 22580 sequences in the IMR90 cell line, but in github, your IMR90 cell line has 22580 sequences in every directions. And in different directions, many sequences are repeated. Is my understanding wrong?

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ZhangPY-bioinformatics commented 3 years ago

Thank you very much for your teaching, but why there are 22580 sequences in each direction, in the section "Prediction ability of cell line/CBS pair model on a new cell type" in the paper,  there are only 22580 sequences in total.

------------------ 原始邮件 ------------------ 发件人: "linDing-group/Deep-loop" @.>; 发送时间: 2021年10月3日(星期天) 下午4:03 @.>; 抄送: "@@.**@.>; 主题: Re: [linDing-group/Deep-loop] Why there are 22580 sequences in every directions in the IMR90 cell line (#2)

Hi, There must be misunderstanding. Since the same sequence would form a loop structure with other different sequences in different directions, so it is normal for a certain sequence to appear repeatedly.

------------------ 原始邮件 ------------------ 发件人: "linDing-group/Deep-loop" @.>; 发送时间: 2021年10月3日(星期天) 中午12:11 @.>; @.***>; 主题: [linDing-group/Deep-loop] Why there are 22580 sequences in every directions in the IMR90 cell line (#2)

I'm sorry to disturb you, but I encountered something very puzzled while studying your paper. You mentioned in your paper that there are 22580 sequences in the IMR90 cell line, but in github, your IMR90 cell line has 22580 sequences in every directions. And in different directions, many sequences are repeated. Is my understanding wrong?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

linDing-group commented 3 years ago

Thanks. Because the model we built can predict loops in 4 directions. So, in the IMR90 cell line, loops in different directions (FF, FR, RF, RR) all contain 22,580 sequences. Please check.

------------------ 原始邮件 ------------------ 发件人: "linDing-group/Deep-loop" @.>; 发送时间: 2021年10月3日(星期天) 下午4:10 @.>; @.**@.>; 主题: Re: [linDing-group/Deep-loop] Why there are 22580 sequences in every directions in the IMR90 cell line (#2)

Thank you very much for your teaching, but why there are 22580 sequences in each direction, in the section "Prediction ability of cell line/CBS pair model on a new cell type" in the paper,  there are only 22580 sequences in total.

------------------ 原始邮件 ------------------ 发件人: "linDing-group/Deep-loop" @.>; 发送时间: 2021年10月3日(星期天) 下午4:03 @.>; 抄送: "@@.**@.>; 主题: Re: [linDing-group/Deep-loop] Why there are 22580 sequences in every directions in the IMR90 cell line (#2)

Hi,
There must be misunderstanding. Since the same sequence would form a loop structure with other different sequences in different directions, so it is normal for a certain sequence to appear repeatedly.

------------------ 原始邮件 ------------------
发件人: "linDing-group/Deep-loop" @.>;
发送时间: 2021年10月3日(星期天) 中午12:11
@.>;
@.***>;
主题: [linDing-group/Deep-loop] Why there are 22580 sequences in every directions in the IMR90 cell line (#2)

I'm sorry to disturb you, but I encountered something very puzzled while studying your paper. You mentioned in your paper that there are 22580 sequences in the IMR90 cell line, but in github, your IMR90 cell line has 22580 sequences in every directions. And in different directions, many sequences are repeated. Is my understanding wrong?

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ZhangPY-bioinformatics commented 3 years ago

Thank you for your careful guidance. I have understood the above problem. Thanks again.

------------------ 原始邮件 ------------------ 发件人: "linDing-group/Deep-loop" @.>; 发送时间: 2021年10月3日(星期天) 下午5:12 @.>; 抄送: "@@.**@.>; 主题: Re: [linDing-group/Deep-loop] Why there are 22580 sequences in every directions in the IMR90 cell line (#2)

Thanks. Because the model we built can predict loops in 4 directions. So, in the IMR90 cell line, loops in different directions (FF, FR, RF, RR) all contain 22,580 sequences. Please check.

------------------ 原始邮件 ------------------ 发件人: "linDing-group/Deep-loop" @.>; 发送时间: 2021年10月3日(星期天) 下午4:10 @.>; @.**@.>; 主题: Re: [linDing-group/Deep-loop] Why there are 22580 sequences in every directions in the IMR90 cell line (#2)

Thank you very much for your teaching, but why there are 22580 sequences in each direction, in the section "Prediction ability of cell line/CBS pair model on a new cell type" in the paper,
 there are only 22580 sequences in total.

------------------ 原始邮件 ------------------
发件人: "linDing-group/Deep-loop" @.>;
发送时间: 2021年10月3日(星期天) 下午4:03
@.>;
抄送: "@@.**@.>;
主题: Re: [linDing-group/Deep-loop] Why there are 22580 sequences in every directions in the IMR90 cell line (#2)

Hi,
There must be misunderstanding. Since the same sequence would form a loop structure with other different sequences in different directions, so it is normal for a certain sequence to appear repeatedly.

------------------ 原始邮件 ------------------
发件人: "linDing-group/Deep-loop" @.>;
发送时间: 2021年10月3日(星期天) 中午12:11
@.>;
@.***>;
主题: [linDing-group/Deep-loop] Why there are 22580 sequences in every directions in the IMR90 cell line (#2)

I'm sorry to disturb you, but I encountered something very puzzled while studying your paper. You mentioned in your paper that there are 22580 sequences in the IMR90 cell line, but in github, your IMR90 cell line has 22580 sequences in every directions. And in different directions, many sequences are repeated. Is my understanding wrong?

—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub, or unsubscribe.
Triage notifications on the go with GitHub Mobile for iOS or Android.
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You are receiving this because you authored the thread.
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— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.