s175573 / GIANA

Ultrafast TCR clustering algorithm based on geometric isometry
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Stringency of thresholds #17

Open CSree opened 2 weeks ago

CSree commented 2 weeks ago

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,

Thanks a lot, in advance Chai

s175573 commented 2 weeks ago

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,

Thanks a lot, in advance Chai

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