Comments (6)
In GitLab by @szabogtamas on Jan 24, 2020, 20:08
marked the task What sequences to use (TCRA/B primary only?) as completed
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In GitLab by @szabogtamas on Jan 24, 2020, 20:08
marked the task What sequences to use (TCRA/B primary only?) as incomplete
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In GitLab by @szabogtamas on Jan 24, 2020, 20:13
For sequence logos I would consider the primary alpha+beta only. The only exception is groups made with tcrdist maybe. Here, I would want to show a sequence logo of the closest chains that are not necessarily the primary alpha and beta.
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In GitLab by @szabogtamas on Jan 24, 2020, 20:14
As to the lacking chains: I would just mark them with 'XXXXXXXXXXXXXXXX' just like for sequence alignment. But this is only an initial idea, maybe we can come up with something better later on.
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Possibly also include V & D genes into sequence logo.
Example from Dash et al. (2017):
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in sc-best-practices, they use the palmotif
library. It looks pretty straightforward
https://www.sc-best-practices.org/air_repertoire/clonotype.html#motif-sequence-analysis
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Related Issues (20)
- If integer field is None, writing AIRR files fails HOT 1
- tl.define_clonotypes within_group parameter returns ValueError HOT 1
- Integrate TCRdist3 HOT 5
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- ir_dist alignment stuck HOT 4
- IEDB database cdr3_aa stored as junction_aa HOT 10
- Unclear default value for the Hamming Distance cut-off HOT 1
- Dandelion interoperability
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- Add the Morisita-Horn index for repertoire overlap similarity scores HOT 1
- Sorting logic in `index_chains()` HOT 3
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- "read_10x_vdj" not loading data properly HOT 2
- clone definition purely using CDR3 sequence HOT 2
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- When running 'ir.tl.define_clonotypes' on MacOS14.4.1, I've got an Error:module 'os' has no attribute 'sched_getaffinity' HOT 2
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