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Add psite estimation with plastid #21

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pinin4fjords opened this issue Feb 19, 2024 · 4 comments
Closed

Add psite estimation with plastid #21

pinin4fjords opened this issue Feb 19, 2024 · 4 comments
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enhancement New feature or request

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@pinin4fjords
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Description of feature

See https://plastid.readthedocs.io/en/latest/generated/plastid.bin.psite.html#module-plastid.bin.psite

Add a plastid/psite module to nf-core/modules, and then here.

@pinin4fjords pinin4fjords added the enhancement New feature or request label Feb 19, 2024
@pinin4fjords pinin4fjords added this to the v1.10 milestone Feb 19, 2024
@JackCurragh
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This is likely a valid tool to use but relating to my recent comment on #24 these older offset predictors don't quite work for certain kinds of samples.

There are a newer kind of P-Site predictors coming about that do it on a read-by-read basis rather than read length-by-read length. For example, psite. The paper has just one figure so you may be able to see how it works for MNase data.

@pinin4fjords
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Thanks! Plastid was specifically requested in our agreement with Altos, but could you make a separate issue for Psite? A quick look suggests it's not in Bioconda yet, so that will be the first job.

@JackCurragh
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Is this still needed for v1.10? What does it add that the tools that we have atm don't provide? It is my understanding that each 'Ribo-Seq specific' tool that we have already does this step in their own way. Is Plastid desired for some other reason?

@pinin4fjords
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Yep, you may be right. I'll remove it from the milestone.

@pinin4fjords pinin4fjords removed this from the v1.1.0 milestone Apr 17, 2024
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