Stringency of thresholds

[CSree]

Hi Bo,
I ran giana query on many input files related to covid and got results.
In the query results after running agianst the hc100 ref, many of them have the following:
"sampleExport:TestReal-HIP01160"

Does this mean the seq did not match a COVID related one?

I notice that the functions that process the input file have the option to choose the top 10000 [or n number] tcr seqs based on their frequency.
However my lab dosent want to discard any sequences. They want to compare even low frequency sequences that match to covid. So the obvious issue after quering is the humungous number or sequences in the final result.
In your opinion,

• can the thresholds of the query be set to be more stringent?
• I see that the default is thr=7, and thr_s=3.3
• Is there a way to ensure only 100% matches to covid sequence are included in the output? Not even a single mismatch?
• Any other way that the results can be pruned to include only the most relevant sequences.

Thanks a lot, in advance
Chai

[s175573]

If you increase thr_s to 4.0, that will force identical match. Best, Bo

…

________________________________ From: CSree ***@***.***> Sent: Monday, November 4, 2024 12:45 PM To: s175573/GIANA ***@***.***> Cc: Subscribed ***@***.***> Subject: [External][s175573/GIANA] Stringency of thresholds (Issue #17) Hi Bo, I ran giana query on many input files related to covid and got results. In the query results after running agianst the hc100 ref, many of them have the following: "sampleExport:TestReal-HIP01160" Does this mean the seq did not match a COVID related one? I notice that the functions that process the input file have the option to choose the top 10000 [or n number] tcr seqs based on their frequency. However my lab dosent want to discard any sequences. They want to compare even low frequency sequences that match to covid. So the obvious issue after quering is the humungous number or sequences in the final result. In your opinion, * can the thresholds of the query be set to be more stringent? * I see that the default is thr=7, and thr_s=3.3 * Is there a way to ensure only 100% matches to covid sequence are included in the output? Not even a single mismatch? * Any other way that the results can be pruned to include only the most relevant sequences. Thanks a lot, in advance Chai — Reply to this email directly, view it on GitHub<#17>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AKWYQC5NWCT4UC3SEFE5OMTZ66QDTAVCNFSM6AAAAABREZBMLSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGYZTGNBUG42DMNQ>. You are receiving this because you are subscribed to this thread.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**.