CRISPRESSO2 Web App Submission Issues

[andrewrvh2]

I am trying to use the CRISPRESSO2 web application (as I have many times in the past), and when I hit submit the page doesn't change at all. After a few minutes it changes to running the analysis but stays there for over 20 minutes. This has been my issues for the last 3 days. It was not a problem last week.

[Colelyman]

Hi @andrewrvh2,

Thank you for using CRISPResso and for letting us know about the issue. We did an upgrade to the website that has led to these issues, we are working on getting it fixed. Thank you for your patience, and hope to have this resolved by the end of the day!

Thank you,
Cole

[Colelyman]

Hi @andrewrvh2,

Would you mind trying to submit your run again? We made some changes yesterday that will hopefully improve the reliability of the website.

Thanks,
Cole

[andrewrvh2]

It seems to be working now, thanks! Were there any other changes made? I reran a sample from before using the same parameters and files as before and the results are slightly different now. Thanks so much for your help! Best, Andy

…

________________________________ From: Cole Lyman ***@***.***> Sent: Thursday, April 2, 2026 3:36 PM To: pinellolab/CRISPResso2 ***@***.***> Cc: Vanden Heuvel, Andy ***@***.***>; Mention ***@***.***> Subject: [External]Re: [pinellolab/CRISPResso2] CRISPRESSO2 Web App Submission Issues (Issue #632) You don't often get email from ***@***.*** Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> [https://avatars.githubusercontent.com/u/1154533?s=20&v=4]Colelyman left a comment (pinellolab/CRISPResso2#632)<#632 (comment)> Hi @andrewrvh2<https://github.com/andrewrvh2>, Would you mind trying to submit your run again? We made some changes yesterday that will hopefully improve the reliability of the website. Thanks, Cole — Reply to this email directly, view it on GitHub<#632?email_source=notifications&email_token=BMVIDB6DY3VV3JEFTKBHKXL4T26MVA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTIMJYGAYDKOJYHAZKM4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLDGN5XXIZLSL5RWY2LDNM#issuecomment-4180059882>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BMVIDB7ZYGI2ZHIDMUE5E2T4T26MVAVCNFSM6AAAAACXJNIVB2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DCOBQGA2TSOBYGI>. You are receiving this because you were mentioned.Message ID: ***@***.***> ** This email originated from an EXTERNAL sender to CHOP. Proceed with caution when replying, opening attachments, or clicking links. Do not disclose your CHOP credentials, employee information, or protected health information to a potential hacker**.

[Colelyman]

Glad to hear that it is working for you, please feel free to reach out anytime you are having trouble.

The update is using a pre-release of CRISPResso2 v2.3.4, which has some additional plots and a redesign of the report. There are also some bug fixes that may change the quantification at the ends of sequences, but these should be rare. Do you mind if I ask what kinds of differences you are seeing?

Thanks,
Cole

[andrewrvh2]

Hey Cole, To give an example of the differences: Prior to update: NHEJ: 0.25 HDR: 38.61 Imperfect HDR: 0.5 After update: NHEJ: 0.25 HDR: 37.20 Imperfect HDR: 1.91 The settings used are: Cas9, Paired End reads, sgRNA, amplicon, expected amplicon, and 90% minimum homology for alignment to amplicon. Everything else is unchanged. Do you know what I can change to try to get the same values as before for consistency (rather than having to go back and reanalyze hundreds of samples). Thanks for your help! Andy

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________________________________ From: Cole Lyman ***@***.***> Sent: Thursday, April 2, 2026 6:06 PM To: pinellolab/CRISPResso2 ***@***.***> Cc: Vanden Heuvel, Andy ***@***.***>; Mention ***@***.***> Subject: [External]Re: [pinellolab/CRISPResso2] CRISPRESSO2 Web App Submission Issues (Issue #632) You don't often get email from ***@***.*** Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> [https://avatars.githubusercontent.com/u/1154533?s=20&v=4]Colelyman left a comment (pinellolab/CRISPResso2#632)<#632 (comment)> Glad to hear that it is working for you, please feel free to reach out anytime you are having trouble. The update is using a pre-release of CRISPResso2 v2.3.4, which has some additional plots and a redesign of the report. There are also some bug fixes that may change the quantification at the ends of sequences, but these should be rare. Do you mind if I ask what kinds of differences you are seeing? Thanks, Cole — Reply to this email directly, view it on GitHub<#632?email_source=notifications&email_token=BMVIDB7LUL3V4EHXHGA2OVT4T3QAHA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTIMJYGA3TGOJWGM32M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLDGN5XXIZLSL5RWY2LDNM#issuecomment-4180739637>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BMVIDBYXKNQLJRY5PCWPVR34T3QAHAVCNFSM6AAAAACXJNIVB2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DCOBQG4ZTSNRTG4>. You are receiving this because you were mentioned.Message ID: ***@***.***> ** This email originated from an EXTERNAL sender to CHOP. Proceed with caution when replying, opening attachments, or clicking links. Do not disclose your CHOP credentials, employee information, or protected health information to a potential hacker**.

[Colelyman]

Hi Andy,

Thank you, would you mind sending the parameters you used for these runs? My hunch is that there was a fix in how the HDR sequence was aligned, and we should be able to correct for that to match the behavior of the previous version.

If you are able to share your data (or a subset of it) that would be helpful as well. If you would rather not share it publicly, you can email us at support@edilytics.com.

Thank you,
Cole