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broadinstitute / SpliceAI-lookup

Website for checking SpliceAI and Pangolin scores:
https://spliceailookup.broadinstitute.org
MIT License
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follow up of issue #67, #69 #84

Open HJin2024 opened 1 week ago

HJin2024 commented 1 week ago

I have a similar situation reported in the issue #67 & #69. I would like to find out how I can check if the SpliceAI scores are real or due to the technical artefact? Is there a way to check this on SpliceAI webpage? Thanks a lot

bw2 commented 1 week ago

When you enter your variant, do you see the warning described in https://github.com/broadinstitute/SpliceAI-lookup/issues/69 ? image

HJin2024 commented 1 week ago

Yes, I do. So I want to check if the delta score is due to the technical artefact or not. How do I check?

Thanks a lot Huilin

From: Ben Weisburd @.> Sent: 08 November 2024 15:07 To: broadinstitute/SpliceAI-lookup @.> Cc: Jin Huilin @.>; Author @.> Subject: Re: [broadinstitute/SpliceAI-lookup] follow up of issue #67, #69 (Issue #84)

When you enter your variant, do you see the warning described in

69https://scanmail.trustwave.com/?c=8248&d=5amu5x0g0Nwbp0YJaeiY4i5EXwOHmP9APw-JkuoiOA&u=https%3a%2f%2fgithub%2ecom%2fbroadinstitute%2fSpliceAI-lookup%2fissues%2f69 ?

image.png (view on web)https://scanmail.trustwave.com/?c=8248&d=5amu5x0g0Nwbp0YJaeiY4i5EXwOHmP9APwmNlrAkaQ&u=https%3a%2f%2fgithub%2ecom%2fuser-attachments%2fassets%2fd01e4ef8-dd0d-4ad0-9d3f-cf0e62997ecb

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bw2 commented 1 week ago

I was thinking of adding a table like the example in https://github.com/broadinstitute/SpliceAI-lookup/issues/69#issue-2172730864

image

Do you agree a table like this would address your question?

HJin2024 commented 1 week ago

Yes definitely. The reason I raised this issue here is to get a table like that. Is it possible for SpliceAi provide the table automatically with a link in the cases like this?

Thanks a lot Huilin

From: Ben Weisburd @.> Sent: 08 November 2024 18:11 To: broadinstitute/SpliceAI-lookup @.> Cc: Jin Huilin @.>; Author @.> Subject: Re: [broadinstitute/SpliceAI-lookup] follow up of issue #67, #69 (Issue #84)

I was thinking of adding a table like the example in

69 (comment)https://scanmail.trustwave.com/?c=8248&d=2tSu59z7LgSRTixRYsK6JxeVUz1ergswaiBp7EHrPg&u=https%3a%2f%2fgithub%2ecom%2fbroadinstitute%2fSpliceAI-lookup%2fissues%2f69%23issue-2172730864

image.png (view on web)https://scanmail.trustwave.com/?c=8248&d=2tSu59z7LgSRTixRYsK6JxeVUz1ergswaiQ8tUuwPQ&u=https%3a%2f%2fgithub%2ecom%2fuser-attachments%2fassets%2f27d23f08-5f6a-4394-8660-7daaa506e5af

Do you agree a table like this would address your question?

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bw2 commented 1 week ago

I've now added this table to a popup for variants where the warning appears:

image
bw2 commented 1 week ago

For example: https://spliceailookup.broadinstitute.org/#variant=13-21155151-C-CAGTTTTCTTTGTTGCTGACATCTCGGATGTTCTGTCCATGTTTAAGGAACCTTTTACTGGGTA&hg=38&bc=basic&distance=500&mask=0&ra=0

HJin2024 commented 1 week ago

Hi Ben

Many thanks for your time. I like the table and it’s very helpful. But my question is actually how to generate this table for my own variant (chr6-56617985-C-CCT, hg38). I was hoping this table would appear in SpliceAI along with the warning message, just like you did in the example.

KR Huilin

From: Ben Weisburd @.> Sent: 12 November 2024 14:11 To: broadinstitute/SpliceAI-lookup @.> Cc: Jin Huilin @.>; Author @.> Subject: Re: [broadinstitute/SpliceAI-lookup] follow up of issue #67, #69 (Issue #84)

I've now added this table to a popup for variants where the warning appears: image.png (view on web)https://scanmail.trustwave.com/?c=8248&d=o-Kz50ayB3atpdHKuOhl1y_uiYo18DT8y9UNJfRJXw&u=https%3a%2f%2fgithub%2ecom%2fuser-attachments%2fassets%2faca6ebb3-7afd-474c-812e-d7b2b9b675b9

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The information contained in this message and or attachments is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Unless otherwise specified, the opinions expressed herein do not necessarily represent those of Guy's and St Thomas' NHS Foundation Trust or any of its subsidiaries. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and any replies cannot be guaranteed.

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bw2 commented 1 week ago

It was showing cached results from before the feature was added. If you reload the page, you should see the new tables.

HJin2024 commented 6 days ago

Yes! That’s fabulous! Thanks a million. Will this table be added along with the warning message for other similar variants as well? I just don’t want to trouble you or other SpliceAI colleagues each time for the same query.

KR Huilin

From: Ben Weisburd @.> Sent: 12 November 2024 17:02 To: broadinstitute/SpliceAI-lookup @.> Cc: Jin Huilin @.>; Author @.> Subject: Re: [broadinstitute/SpliceAI-lookup] follow up of issue #67, #69 (Issue #84)

It was showing cached results from before the feature was added. If you reload the page, you should see the new tables.

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bw2 commented 6 days ago

Hi Huilin, yes, the table appears for any variant that has that warning.

HJin2024 commented 6 days ago

Thanks a million!

Huilin

From: Ben Weisburd @.> Sent: 13 November 2024 13:31 To: broadinstitute/SpliceAI-lookup @.> Cc: Jin Huilin @.>; Author @.> Subject: Re: [broadinstitute/SpliceAI-lookup] follow up of issue #67, #69 (Issue #84)

Hi Huilin, yes, the table appears for any variant that has that warning.

— Reply to this email directly, view it on GitHubhttps://scanmail.trustwave.com/?c=8248&d=0Kq05xKO8y-fK3W_eNk7Mwa40Q3FLdqr0hcF1MRv2Q&u=https%3a%2f%2fgithub%2ecom%2fbroadinstitute%2fSpliceAI-lookup%2fissues%2f84%23issuecomment-2473630191, or unsubscribehttps://scanmail.trustwave.com/?c=8248&d=0Kq05xKO8y-fK3W_eNk7Mwa40Q3FLdqr0kZQ05JhjQ&u=https%3a%2f%2fgithub%2ecom%2fnotifications%2funsubscribe-auth%2fBMYSQOGAL4ZYCZHDYUFM5732ANIBBAVCNFSM6AAAAABRNSOG3KVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINZTGYZTAMJZGE. You are receiving this because you authored the thread.Message ID: @.**@.>>

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bw2 commented 6 days ago

Also, based on additional feedback, instead of the warning icon, we now just show the exact position in the main table, along with the icon that brings up the detailed table. [example]

image
amartins1 commented 6 days ago

Hi, When I tried to visualize the example indicated in your message below and clicked on the icon, I did see a table popping up on the bottom left but only partially. It seems that it does not properly fit on the screen of my laptop computer. Impossible to scroll further to the right.Difficult to inspect the full table even when I resize the screen All best; Alexandra

Le Mercredi, Novembre 13, 2024 22:30 CET, Ben Weisburd @.> a écrit:     Also, based on additional feedback, instead of the warning icon, we now just show the exact position in the main table, along with the icon that brings up the detailed table. [example]image.png (view on web) — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.> [ { @.": "http://schema.org", @.": "EmailMessage", "potentialAction": { @.": "ViewAction", "target": "https://github.com/broadinstitute/SpliceAI-lookup/issues/84#issuecomment-2474826939", "url": "https://github.com/broadinstitute/SpliceAI-lookup/issues/84#issuecomment-2474826939", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { @.": "Organization", "name": "GitHub", "url": "https://github.com" } } ] --  Alexandra Martins, PhD, HDR Inserm Researcher (CRHC) Group Leader Inserm UMR 1245 - Cancer and Brain Genomics UFR Santé 22 Bvd Gambetta CS 76183 76183 Rouen Cedex 1 France phone#: + 33 (0)2 35 14 83 14 email: @.*** https://www.researchgate.net/profile/Alexandra_Martins5 ORCID ID: 0000-0003-4322-8497  

bw2 commented 6 days ago

Hi Alexandra, what browser and operating system are you using?

HJin2024 commented 5 days ago

Hi Ben

The table is showing correctly on my laptop for my variant. I use google chrome. And I like the updated version “instead of the warning icon, we now just show the exact position in the main table, along with the icon that brings up the detailed table”!

Thanks a lot Huilin

From: Ben Weisburd @.> Sent: 14 November 2024 00:11 To: broadinstitute/SpliceAI-lookup @.> Cc: Jin Huilin @.>; Author @.> Subject: Re: [broadinstitute/SpliceAI-lookup] follow up of issue #67, #69 (Issue #84)

Hi Alexandra, what browser and operating system are you using?

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The information contained in this message and or attachments is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Unless otherwise specified, the opinions expressed herein do not necessarily represent those of Guy's and St Thomas' NHS Foundation Trust or any of its subsidiaries. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and any replies cannot be guaranteed.

Any review, retransmission,dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any system and destroy any copies.

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bw2 commented 5 days ago

Thanks Huilin

amartins1 commented 5 days ago

Dear Ben, Thanks for your prompt reply In my laptop I use

Le Jeudi, Novembre 14, 2024 01:11 CET, Ben Weisburd @.> a écrit:     Hi Alexandra, what browser and operating system are you using? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.>[ { @.": "http://schema.org", @.": "EmailMessage", "potentialAction": { @.": "ViewAction", "target": "https://github.com/broadinstitute/SpliceAI-lookup/issues/84#issuecomment-2475079172", "url": "https://github.com/broadinstitute/SpliceAI-lookup/issues/84#issuecomment-2475079172", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { @.": "Organization", "name": "GitHub", "url": "https://github.com" } } ] --  Alexandra Martins, PhD, HDR Inserm Researcher (CRHC) Group Leader Inserm UMR 1245 - Cancer and Brain Genomics UFR Santé 22 Bvd Gambetta CS 76183 76183 Rouen Cedex 1 France phone#: + 33 (0)2 35 14 83 14 email: @.*** https://www.researchgate.net/profile/Alexandra_Martins5 ORCID ID: 0000-0003-4322-8497