Add new training for scATAC-seq analysis using SnapATAC2 #4973
Conversation
pavanvidem
changed the title
There was a problem hiding this comment.
Well done @timonschlegel! Very well structured and clearly written.
Please try to resolve my (minor) review comments.
topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.md
Show resolved
Hide resolved
topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.md
Outdated
Show resolved
Hide resolved
topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.md
Outdated
Show resolved
Hide resolved
topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.md
Show resolved
Hide resolved
topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.md
Outdated
Show resolved
Hide resolved
topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.md
Outdated
Show resolved
Hide resolved
| > | ||
| > 4. {% tool [Normalize](toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy2) %} with the following parameters: | ||
| > - {% icon param-file %} *"Annotated data matrix"*: `Anndata log1p` (output of **log1p** {% icon tool %}) | ||
| > - *"Method used for normalization"*: `Denoising using Markov Affinity-based Graph Imputation of Cells (MAGIC) API 'external.pp.magic'` |
There was a problem hiding this comment.
a short intro to MAGIC algorithm with a link to the documentation and citation would be nice.
There was a problem hiding this comment.
good idea, I will add it
topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.md
Show resolved
Hide resolved
|
|
||
|
|
||
| # Conclusion | ||
| {% icon congratulations %} Well done, you’ve made it to the end! You might want to consult your results with this [control history](https://singlecell.usegalaxy.eu/u/timonschlegel/h/test-of-5k-pbmc-tutorial-workflow), or check out the [full workflow](https://singlecell.usegalaxy.eu/u/timonschlegel/w/2combined-snapatac2) for this tutorial. |
There was a problem hiding this comment.
links to the control history and the workflow are invalid. Please check.
There was a problem hiding this comment.
strange, because they do work for me. I have updated my visable name a few days ago, maybe that is causing the issues? But since I updated the links it works for me.
But I have to change the control history anyway before publishing, since I don't have a history that contains the entire process, because make_fragment_file isn't updated yet. And maybe I will also change the workflow, so that each step is listed individually? And I could add the make_bam-file steps as well
topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.md
Outdated
Show resolved
Hide resolved
topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.md
Outdated
Show resolved
Hide resolved
Co-authored-by: Björn Grüning <[email protected]>
There was a problem hiding this comment.
big thanks to @timonschlegel for this great tutorial and workflow
|
@timonschlegel please consider writing a small blog post to announce this tutorial :) |
|
@bgruening I've now made a PR containing the announcement. I hope everything looks okay :) |
Please review :)