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ysora / stripenn

Architectural stripe detection from 3D genome conformation data
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input data #5

Closed BenxiaHu closed 2 years ago

BenxiaHu commented 2 years ago

Hello, Thanks for developing this great tool analyzing Stripe. I have 1 question: the input contact matrix is must be not normalized/balancing contact matrix, right? can I provided iced normalized contact matrix to Stripenn? Best,

ysora commented 2 years ago

You can input either raw/normalized/balancing data. Let me know if you have any issues. FYI, if you have some error running stripenn, please set -n 1 parameter since there is an issue with parallel package. Thanks

Best, Sora

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From: bxhu @.> Sent: Saturday, September 24, 2022 5:34:17 PM To: ysora/stripenn @.> Cc: Subscribed @.***> Subject: [External] [ysora/stripenn] input data (Issue #5)

Hello, Thanks for developing this great tool analyzing Stripe. I have 1 question: the input contact matrix is must be not normalized/balancing contact matrix, right? can I provided iced normalized contact matrix to Stripenn? Best,

— Reply to this email directly, view it on GitHubhttps://github.com/ysora/stripenn/issues/5, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABZHMJVHY66V5XRFMDG5KATV75XVTANCNFSM6AAAAAAQUZZHLE. You are receiving this because you are subscribed to this thread.Message ID: @.***>

BenxiaHu commented 2 years ago

thanks a lot. what is the minimum valid pairs? Are 200million valid pairs enough to call Stripes?

ysora commented 2 years ago

Yes, 200M is enough!

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From: bxhu @.> Sent: Saturday, September 24, 2022 6:19:49 PM To: ysora/stripenn @.> Cc: Yoon, Sora @.>; Comment @.> Subject: [External] Re: [ysora/stripenn] input data (Issue #5)

thanks a lot. what is the minimum valid pairs? Are 200million valid pairs enough to call Stripes?

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ysora commented 2 years ago

Minimum is 100~150M I think

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From: bxhu @.> Sent: Saturday, September 24, 2022 6:19:49 PM To: ysora/stripenn @.> Cc: Yoon, Sora @.>; Comment @.> Subject: [External] Re: [ysora/stripenn] input data (Issue #5)

thanks a lot. what is the minimum valid pairs? Are 200million valid pairs enough to call Stripes?

— Reply to this email directly, view it on GitHubhttps://github.com/ysora/stripenn/issues/5#issuecomment-1257074609, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABZHMJTIHMODHKKLJG5R74TV755ALANCNFSM6AAAAAAQUZZHLE. You are receiving this because you commented.Message ID: @.***>

BenxiaHu commented 2 years ago

thanks a lot.