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s175573 / GIANA

Ultrafast TCR clustering algorithm based on geometric isometry
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Two strange behaviors encountered while running GIANA4.py #14

Closed snaketron closed 3 weeks ago

snaketron commented 3 weeks ago

  1. GIANA drops singleton CDR3 sequences from the output and sorts the output CDR3s. Is this a desired behavior, it makes downstream analysis complex. (this is made more difficult due to 2.)

  2. (Correction) there are 4 identical CDR3 sequences in input (no V-gene info) -> in the output there are two blocks of these 4 CDR3 sequences with two different cluster IDs. (I can provide exampl)

s175573 commented 3 weeks ago

For your questions:

1. Yes, the goal of GIANA is to find TCRs that can be clustered. It drops singletons. 2. This is a known, small bug in GIANA. It influences a small percentage (<2%) of the TCRs. You may run the bug-fixed 4.1 version, which will be slower. Alternatively, you may fix it post hoc.

From: snaketron @.> Sent: Wednesday, October 30, 2024 1:45 PM To: s175573/GIANA @.> Cc: Subscribed @.***> Subject: [External][s175573/GIANA] Two strange behaviors encountered while running GIANA4.py (Issue #14)

  1. GIANA drops singleton CDR3 sequences from the output and sorts the output CDR3s. Is this a desired behavior, it makes downstream analysis complex. (this is made more difficult due to 2.)

  2. Two blocks of the same CDR3 sequence which are positioned at two contiguous block rows in the input table (e.g. rows 1000-1005 and rows 6000-6005), are assigned into two different clusters. Is this possible? (I can provide an example)

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snaketron commented 3 weeks ago

Cool, thank you!