I am trying to use the CRISPRCloud2 platform that you created to do DRISPR analysis. I

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Fasta file issue about cb2 HOT 16 CLOSED

bennychang2 commented on September 4, 2024

Fasta file issue

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hyunhwan-jeong commented on September 4, 2024

Can you try to run this without the .txt extension? I believe that the file name has to be gRANs-only2.fasta

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bennychang2 commented on September 4, 2024

Hi Hyun-Hwan, Thanks. You are right. It moves forward after I changed the file extension. Thank you very much. Benny From: Hyun-Hwan Jeong ***@***.***> Sent: Wednesday, July 26, 2023 1:55 PM To: hyunhwan-jeong/CB2 ***@***.***> Cc: Chang,Benny ***@***.***>; Author ***@***.***> Subject: [EXTERNAL] Re: [hyunhwan-jeong/CB2] Fasta file issue (Issue #20) THIS EMAIL IS A PHISHING RISK Do you trust the sender? The email address is: ***@***.******@***.***> While this email has passed our filters, we need you to review with caution before taking any action. If the email looks at all suspicious, click the Report a Phish button. Can you try to run this without the .txt extension? I believe that the file name has to be gRANs-only2.fasta — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https:/github.com/hyunhwan-jeong/CB2/issues/20*issuecomment-1652328867__;Iw!!PfbeBCCAmug!jAfaG5BkBVjr6qiEfefvM6V8cFYjqLnLq4pwjEcbtAC0Rwo9EvQHTUsH_-z3OMhclick-E_5iJFIPVoMAAOtNU5B7g$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/BBRCNRTI4YBSDADTJA3XGETXSFRWXANCNFSM6AAAAAA2Y74XXY__;!!PfbeBCCAmug!jAfaG5BkBVjr6qiEfefvM6V8cFYjqLnLq4pwjEcbtAC0Rwo9EvQHTUsH_-z3OMhclick-E_5iJFIPVoMAAMcuCjZxw$>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>> The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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bennychang2 commented on September 4, 2024

Hi Hyun-Hwan

I submitted an analysis last Friday, and the data was successfully uploaded. But I used the link to access the results a few times, and I got:
Processing
The analysis is waiting for its turn or is still going on. Please return to this page later.

Should I continue to wait for it or is there an issue that I should resubmit?
Thanks.

Benny

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hyunhwan-jeong commented on September 4, 2024

Please send me the link to ***@***.*** so that I can take a look. Thank you,

…

On Mon, Jul 31, 2023 at 11:35 AM bennychang2 ***@***.***> wrote: Hi Hyun-Hwan I submitted an analysis last Friday, and the data was successfully uploaded. But I used the link to access the results a few times, and I got: Processing The analysis is waiting for its turn or is still going on. Please return to this page later. Should I continue to wait for it or is there an issue that I should resubmit? Thanks. Benny — Reply to this email directly, view it on GitHub <#20 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEWSZ6FMIVCSGAQBCTORLATXS7NF3ANCNFSM6AAAAAA2Y74XXY> . You are receiving this because you modified the open/close state.Message ID: ***@***.***>

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hyunhwan-jeong commented on September 4, 2024

@bennychang2 I deleted the link on Github.

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bennychang2 commented on September 4, 2024

Thank you. I guess the link is accessible to everyone. Thank you very much.
Let me know whether the analysis is stalled or simply too many requests are being processed.
Thanks

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hyunhwan-jeong commented on September 4, 2024

I passed the link to the person who can access the inside, and I will update you once we figure it out.

…

On Mon, Jul 31, 2023 at 1:43 PM bennychang2 ***@***.***> wrote: Thank you. I guess the link is accessible to everyone. Thank you very much. Let me know whether the analysis is stalled or simply too many requests are being processed. Thanks — Reply to this email directly, view it on GitHub <#20 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEWSZ6BNSSQ3Y46PMX6R2ADXS74EBANCNFSM6AAAAAA2Y74XXY> . You are receiving this because you modified the open/close state.Message ID: ***@***.***>

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bennychang2 commented on September 4, 2024

It's been three days; I wonder if I should submit the job again?

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hyunhwan-jeong commented on September 4, 2024

I haven’t heard back from the team yet, can you try it again? Right now I am out of town and maybe slow to respond until Saturday.

…

On Thursday, August 3, 2023, bennychang2 ***@***.***> wrote: It's been three days; I wonder if I should submit the job again? — Reply to this email directly, view it on GitHub <#20 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEWSZ6GHBFWBRV2SL3W6MEDXTORSXANCNFSM6AAAAAA2Y74XXY> . You are receiving this because you modified the open/close state.Message ID: ***@***.***>

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hyunhwan-jeong commented on September 4, 2024

@bennychang2, sorry for the delay, I was able to check the run, and it has been completed analysis. Are you still seeing the same message? If so, I can send the outputs to your email address. Let me know if you want.

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bennychang2 commented on September 4, 2024

It showed that my webserver is ok; cloudfare is ok, but crispr.nrihub is down. So I could not access my results.

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hyunhwan-jeong commented on September 4, 2024

I was told that something is wrong with the cloudfare, but I can send a result to you (zipped file). please send me your email address to ***@***.*** so that I can send a zipped file that contains a result. Best regards,

…

On Thu, Aug 10, 2023 at 2:34 PM bennychang2 ***@***.***> wrote: It showed that my webserver is ok; cloudfare is ok, but crispr.nrihub is down. So I could not access my results. — Reply to this email directly, view it on GitHub <#20 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEWSZ6BXGHSLX7SYCRDW3XTXUUZVBANCNFSM6AAAAAA2Y74XXY> . You are receiving this because you modified the open/close state.Message ID: ***@***.***>

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bennychang2 commented on September 4, 2024

[email protected]

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bennychang2 commented on September 4, 2024

The QC results showed low mappability values
24.84 and 27.06.
It does not seem to be good!

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hyunhwan-jeong commented on September 4, 2024

Have you checked FASTQC of the FASTQ files? Make sure that FASTQC doesn't show any red flags on per base sequence quality. It's hard to tell why this is happening since we don't store FASTQ files. If you want me to digging, would it be possible that you to share your FASTQ files with me? If you want me to do this, please send me at ***@***.***, and do not send it to any github related email address for your data privacy.

…

On Fri, Aug 11, 2023 at 1:12 PM bennychang2 ***@***.***> wrote: The QC results showed low mappability values 24.84 and 27.06. It does not seem to be good! — Reply to this email directly, view it on GitHub <#20 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEWSZ6BCDRJZSGP4HRSUQZTXUZY2LANCNFSM6AAAAAA2Y74XXY> . You are receiving this because you modified the open/close state.Message ID: ***@***.***>

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bennychang2 commented on September 4, 2024

I think I know what went wrong. I was trying to validate the CRISPRi library that I amplified after transforming clone DNA obtained from Addgene. The library was divided in 2 halves. 83987 has one half and 83988 has the other half.
In trying to validate I amplified the CRISPRi part of the DNA in the pool of clones and send for NGS. Because there are two pools (two halves), so each pool should have only half of the CRISPRi. But as an input I used the complete CRISPRi library. No wonder the mappabilities were low.

But now I do not know how I can get an idea of how the good the amplified half pool represent the original half library. Do you know what software can allow me to do that? Thanks.

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Fasta file issue about cb2 HOT 16 CLOSED

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