Calculation of percent misincorporation

[jchariker]

Your tool is working successfully for me. Thank you for developing it! My question is about the calculation of the y-axis for certain graphs in the output. I'm interested in the percent misincorporation in graphs such as SeC_trnapositionmismatches. These are in the mismatch folder with one text file labeled sigmismatch, and I have been working on the assumption that I could calculate it with the information in that file, but I cannot seem to do it. ...at least to match what I see in the images that are created.
Thanks for any help you can give!
Julia

[andrewdholmes]

All the misincorporation data is in the "expname-coverage.txt" file, should be able to get mismatch levels and what the mismatches are in terms of individual bases from that.

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On Sun, May 7, 2023 at 1:53 PM jchariker ***@***.***> wrote: Your tool is working successfully for me. Thank you for developing it! My question is about the calculation of the y-axis for certain graphs in the output. I'm interested in the percent misincorporation in graphs such as SeC_trnapositionmismatches. These are in the mismatch folder with one text file labeled sigmismatch, and I have been working on the assumption that I could calculate it with the information in that file, but I cannot seem to do it. ...at least to match what I see in the images that are created. Thanks for any help you can give! Julia — Reply to this email directly, view it on GitHub <#23>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEHEMLSU6OO7TR4DFRAQPF3XFADUBANCNFSM6AAAAAAXZD6M7Q> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[jchariker]

Thank you for pointing me in the right direction! I was able to find the appropriate file and recreate the values you are displaying in your graphs. Julia From: andrewdholmes ***@***.***> Sent: Friday, May 12, 2023 1:38 PM To: UCSC-LoweLab/tRAX ***@***.***> Cc: Chariker, Julia ***@***.***>; Author ***@***.***> Subject: Re: [UCSC-LoweLab/tRAX] Calculation of percent misincorporation (Issue #23) CAUTION: This email originated from outside of our organization. Do not click links, open attachments, or respond unless you recognize the sender's email address and know the contents are safe. All the misincorporation data is in the "expname-coverage.txt" file, should be able to get mismatch levels and what the mismatches are in terms of individual bases from that.

On Sun, May 7, 2023 at 1:53 PM jchariker ***@***.***> wrote: Your tool is working successfully for me. Thank you for developing it! My question is about the calculation of the y-axis for certain graphs in the output. I'm interested in the percent misincorporation in graphs such as SeC_trnapositionmismatches. These are in the mismatch folder with one text file labeled sigmismatch, and I have been working on the assumption that I could calculate it with the information in that file, but I cannot seem to do it. ...at least to match what I see in the images that are created. Thanks for any help you can give! Julia — Reply to this email directly, view it on GitHub <#23>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEHEMLSU6OO7TR4DFRAQPF3XFADUBANCNFSM6AAAAAAXZD6M7Q> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

— Reply to this email directly, view it on GitHub<#23 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACYK6ZO4WGDAIU73KCJAC5DXFZYPRANCNFSM6AAAAAAXZD6M7Q>. You are receiving this because you authored the thread.Message ID: ***@***.***>