CRISPResso2 cannot detect HDR

[lvelve0901]

I have tried to use CRISPResso version 2.0.31 to process my NGS HDR data. For some reason, I input the HDR sequence as the format of the amplicon but in the output file, my HDR sequence are still detected as NHEJ, in the Figure 9 9.Reference.Alleles_frequency_table_around_sgRNA_XXXXXX.pdf, I can clearly see my HDR sequences are listed inside. Any suggestion of what could be wrong? My aplicon is at the long side which is 260 bps and the illumina sequence read is only 150 bps from one end. I have two other datasetd with amplicon 190 bps and 240 bps and CRISPResso are able to detect and analyze HDR for both.

[kclem]

Hi @lvelve0901 thanks for using CRISPResso!

Would you mind updating to a recent release to see if the problem is fixed? The current release is v.2.2.6.

For the HDR sequence, you'll have to provide the entire amplicon sequence that includes the HDR sequence, not just the HDR subsequence.

I'm not sure exactly what is going wrong. Do you think you could update to v2.2.6 and post (or send me an email):

1. the CRISPResso command you used
2. a screenshot of your Figure 9 with the problematic sequences circled

[lvelve0901]

Hi Kendell,

In the GitHub deposit, the version is 2.0.20b. https://github.com/pinellolab/CRISPResso2 https://github.com/pinellolab/CRISPResso2 Could you please let me know where to download 2.2.6?

Thanks.

Best, Honglue

在 2022年1月31日，上午7:58，Kendell Clement @.***> 写道：

Hi @lvelve0901 https://github.com/lvelve0901 thanks for using CRISPResso!

Would you mind updating to a recent release to see if the problem is fixed? The current release is v.2.2.6.

For the HDR sequence, you'll have to provide the entire amplicon sequence that includes the HDR sequence, not just the HDR subsequence.

I'm not sure exactly what is going wrong. Do you think you could update to v2.2.6 and post (or send me an email):

the CRISPResso command you used a screenshot of your Figure 9 with the problematic sequences circled — Reply to this email directly, view it on GitHub https://github.com/pinellolab/CRISPResso2/issues/193#issuecomment-1025933466, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG4MBOON3CPFLNR3CF2LZXDUY2WS3ANCNFSM5NFO5DRQ. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you were mentioned.

[kclem]

All releases can be found in the 'Tags' section.

If you've installed using conda you should be able to update by running conda update crispresso2. Note that one of the changes in 2.2 is that we've switched to python 3, so it may be best to delete your old conda environment entirely and reinstall so that the correct python version can be used: conda create -n crispresso2_env -c bioconda crispresso2

Let me know if that works!

[lvelve0901]

Dear Kendell,

Is there a way to send you the command and screenshot without posting to the GitHub for now?

Best, Honglue

在 2022年1月31日，上午11:17，Kendell Clement @.***> 写道：

All releases can be found in the 'Tags x-msg://3/tags/' section.

If you've installed using conda you should be able to update by running conda update crispresso2. Note that one of the changes in 2.2 is that we've switched to python 3, so it may be best to delete your old conda environment entirely and reinstall so that the correct python version can be used: conda create -n crispresso2_env -c bioconda crispresso2

Let me know if that works!

— Reply to this email directly, view it on GitHub https://github.com/pinellolab/CRISPResso2/issues/193#issuecomment-1026120587, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG4MBOJRA6RNIDBSQRPHIKDUY3N55ANCNFSM5NFO5DRQ. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you were mentioned.

[kclem]

Sure, you can email me at [email protected]

[kclem]

We're closing this issue because it hasn't been updated recently. If this issue still exists, please reopen this issue and we'll look into it!