diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index 4cbf4a428a8913..e3993006fe7d06 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -610,6 +610,12 @@ desmond-jasper: name: Desmond Jasper joined: 2020-04 +dianichj: + name: Diana Chiang Jurado + email: dianachj@informatik.uni-freiburg.de + orcid: 0000-0002-5857-1477 + joined: 2024-08 + dirowa: name: Donny Vrins joined: 2021-10 diff --git a/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.md b/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.md index 972f9d4a0d9396..8a0f53d45bb00e 100644 --- a/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.md +++ b/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.md @@ -39,6 +39,7 @@ contributors: - hrhotz - mtekman - pavanvidem +- dianichj gitter: Galaxy-Training-Network/galaxy-single-cell @@ -489,6 +490,28 @@ To create this table, we need to: > - *"What to inspect?"*: `Key-indexed annotation of variables/features (var)` > > 12. Inspect the generated file and check if the mitochondrial annotation has been added +> +> > +> > +> > 1. How can I filter genes like ribosomal protein genes or non-protein coding genes that might interfere with my downstream analysis? +> > 2. What steps should I take to identify these genes in my data? +> > +> > > +> > > +> > > 1. To filter genes such as ribosomal protein genes or non-protein coding genes, follow these steps: +> > > +> > > - Use the gene annotation file as you did for mitochondrial genes. +> > > - Adjust the expression from `$1 ~ /^MT-/` to `$1 ~ /^RP/` for ribosomal protein genes or `$1 ~ /^LINC/` for non-protein coding genes. +> > > - Create a tabular file for the new annotation column, e.g., `rpgene` for ribosomal protein genes or `lincrna` for long non-coding RNAs. +> > > ``` +> > > rpgene +> > > ``` +> > > - Add your new gene annotation to the data matrix using the {% tool [Manipulate Anndata](toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0) %} tool, similar to step 7 of the mitochondrial annotation process. +> > > - Inspect your AnnData to confirm the new gene annotations are correctly added. +> > > 2. Long Non-Coding RNAs often start with "LINC" followed by a number, while Ribosomal Protein Genes typically start with "RP". Be aware that some non-ribosomal genes also start with "RP" and are associated with conditions like Retinitis Pigmentosa. If these genes are relevant, annotate 'RP' genes carefully. +> > > +> > {: .solution} +> {: .question} {: .hands_on} We can now compute QC metrics on the `AnnData` object.