follow up of issue #67, #69 #84
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When you enter your variant, do you see the warning described in |
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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
#69<https://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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I was thinking of adding a table like the example in 
Do you agree a table like this would address your question? |
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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
added a commit
to bw2/SpliceAI
that referenced
this issue
Nov 11, 2024
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I've now added this table to a popup for variants where the warning appears: 
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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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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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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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Hi Huilin, yes, the table appears for any variant that has that warning. |
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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.
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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] 
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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)
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Hi Alexandra, what browser and operating system are you using? |
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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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Thanks Huilin |
|
Dear Ben,
Thanks for your prompt reply
In my laptop I use
- mozilla firefox (browser)
- microsoft windows 11 family (operating system)
All best,
Alexandra
Le Jeudi, Novembre 14, 2024 01:11 CET, Ben Weisburd ***@***.***> a écrit:
Hi Alexandra, what browser and operating system are you using?
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--
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
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@amartins1 I have not been able to reproduce the issue in Firefox. |
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Just in case it's still an issue on some browsers, I've added an option to display the table in a separate popup dialog: 
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Great. Thanks!
Le Mercredi, Décembre 04, 2024 15:46 CET, Ben Weisburd ***@***.***> a écrit:
Just in case it's still an issue on some browsers, I've added an option to display the table in a separate popup dialog:image.png (view on web) image.png (view on web)
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Alexandra Martins, PhD, HDR
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Group Leader
INSERM U1245, Cancer and Brain Genomics (CBG)
UFR Santé, Univ Rouen Normandie
22 Boulevard Gambetta
76183 Rouen
France
phone# (office): + 33 0(2) 35 14 83 14
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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
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