scirpy
scirpy copied to clipboard
scverse
Sequence Logos
In GitLab by @grst on Jan 24, 2020, 14:06
Here's a quite recent re-implementation of sequence logos in Python that looks promising: https://github.com/jbkinney/logomaker
We will also require an algorithm for multiple sequence alignment in addition to the pairwise one that we have already.
Things to discuss:
- [ ] What sequences to use (TCRA/B primary only?)
- [ ] What happens if a cell lacks the alpha/beta chain?
In GitLab by @szabogtamas on Jan 24, 2020, 20:08
marked the task What sequences to use (TCRA/B primary only?) as completed
In GitLab by @szabogtamas on Jan 24, 2020, 20:08
marked the task What sequences to use (TCRA/B primary only?) as incomplete
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.
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.
Possibly also include V & D genes into sequence logo.
Example from Dash et al. (2017):
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