From 50b713e44843f2861e31fe92b79acc7ca1c04e34 Mon Sep 17 00:00:00 2001 From: Timon Schlegel Date: Sun, 23 Jun 2024 20:47:28 +0000 Subject: [PATCH] updated zenodo files and fixed snippet issue --- .../scatac-standard-processing-snapatac2/data-library.yaml | 4 ++++ .../scatac-standard-processing-snapatac2/tutorial.md | 4 +++- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/data-library.yaml b/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/data-library.yaml index 5e0d4357b3daf6..7f120d729e25df 100644 --- a/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/data-library.yaml +++ b/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/data-library.yaml @@ -25,3 +25,7 @@ items: src: url ext: auto info: https://zenodo.org/records/11369811 + - url: https://zenodo.org/api/records/11369811/files/BAM_500-PBMC.bam/content + src: url + ext: auto + info: https://zenodo.org/records/11369811 \ No newline at end of file diff --git a/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.md b/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.md index 65e1202da0d3ba..e3680a3f14374b 100644 --- a/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.md +++ b/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.md @@ -151,7 +151,7 @@ SnapATAC2 requires 3 input files for the standard pathway of processing: > > fragment file > > 1. Import the file `BAM_500-PBMC` from [Zenodo]({{ page.zenodo_link }}) or from the shared data library > > ``` -> > {{ page.zenodo_link }}/files/atac_pbmc_5k_nextgem_fragments.tsv +> > {{ page.zenodo_link }}/files/BAM_500-PBMC.bam > > ``` > > - This dataset contains mapped reads in the `BAM` format. > > - It was generated by following the tutorial ["Pre-processing of 10X Single-Cell ATAC-seq Datasets"]( {% link topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.md %} ) until the output of {% tool [Map with BWA-MEM](toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18) %} @@ -885,7 +885,9 @@ To manually annotate the *Leiden* clusters, we will need to perform multiple ste > 7. Rename the generated file to `Cell type annotation` and {% icon galaxy-eye %} inspect the file to check if the replacement was successful > - check if the datatype is set to `tabular` > - you may need to change the datatype manually +> > {% snippet faqs/galaxy/datasets_change_datatype.md datatype="tabular"%} +> > 8. {% tool [Manipulate AnnData](toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0) %} with the following parameters: > - {% icon param-file %} *"Annotated data matrix"*: `Anndata 5k PBMC gene_matrix magic UMAP` > - *"Function to manipulate the object"*: `Add new annotation(s) for observations or variables`