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hukai916 / scATACpipe

MIT License
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labelling cell clusters from 10XGENOMICS workflow #1

Closed davidlyon3 closed 1 year ago

davidlyon3 commented 1 year ago

Thank you for the nice pipeline. I am a beginning in single cell bio. but I manage to run this 10XGENOMICS workflow pipeline but realize after many hours that the pipeline does not appear to label the PBMC clusters automatically from what I can see.

Can you show me exactly (since I am a beginning you may need to spell this out) how to label the PBMC Cell Clusters.

Thank you in advance.

hukai916 commented 1 year ago

Hi @davidlyon3, thanks for your interests.

To customize the labelings, you may need to edit the corresponding R script that was used to create the plot. Nextflow creates a separate work directory for each task, which are saved under work/ directory by default. And the results are soft-linked to the results/ folder by default. You can use the ls -la command to show the actual working folder. For example, ls -la results/archr_clustering/jpeg/Clusters_heatmap.jpg will show you the full actual path to it. If you navigate to the actual work folder, you will see a run.R script, which was used to create the plot. You can edit that file and perform custom analysis from there.

Let me know if make any sense,

davidlyon3 commented 1 year ago

Very useful.

Thank you very much again.