diff --git a/topics/epigenetics/tutorials/atac-seq/data-library.yaml b/topics/epigenetics/tutorials/atac-seq/data-library.yaml new file mode 100644 index 0000000000000..9494bc73dc78e --- /dev/null +++ b/topics/epigenetics/tutorials/atac-seq/data-library.yaml @@ -0,0 +1,29 @@ +--- +destination: + type: library + name: GTN - Material + description: Galaxy Training Network Material + synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org +items: +- name: Epigenetics + description: DNA methylation is an epigenetic mechanism used by higher eukaryotes + and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and + gene silencing of germline specific gene and repetitive elements. + items: + - name: ATAC-Seq data analysis + items: + - name: 'DOI: 10.5281/zenodo.3862793' + description: latest + items: + - url: https://zenodo.org/api/files/b205aa3d-919b-4fbb-a8dd-3ae01d5daa91/ENCFF933NTR.bed.gz + src: url + ext: gz + info: https://zenodo.org/record/3862793 + - url: https://zenodo.org/api/files/b205aa3d-919b-4fbb-a8dd-3ae01d5daa91/SRR891268_chr22_enriched_R1.fastq.gz + src: url + ext: gz + info: https://zenodo.org/record/3862793 + - url: https://zenodo.org/api/files/b205aa3d-919b-4fbb-a8dd-3ae01d5daa91/SRR891268_chr22_enriched_R2.fastq.gz + src: url + ext: gz + info: https://zenodo.org/record/3862793 diff --git a/topics/epigenetics/tutorials/atac-seq/tutorial.md b/topics/epigenetics/tutorials/atac-seq/tutorial.md index 210b8027c939f..b71b2de2b0be0 100644 --- a/topics/epigenetics/tutorials/atac-seq/tutorial.md +++ b/topics/epigenetics/tutorials/atac-seq/tutorial.md @@ -2,7 +2,7 @@ layout: tutorial_hands_on title: ATAC-Seq data analysis -zenodo_link: "https://zenodo.org/record/3270536" +zenodo_link: https://zenodo.org/record/3862793 questions: - Which DNA regions are accessible in the human lymphoblastoid cell line GM12878? - How to analyse and visualise ATAC-Seq data? @@ -62,12 +62,12 @@ We first need to download the sequenced reads (FASTQs) as well as other annotati > > {% include snippets/create_new_history.md %} > -> 2. Import the files from [Zenodo](https://zenodo.org/record/3270536) and [ENCODE](https://www.encodeproject.org/) or from the shared data library +> 2. Import the files from [Zenodo](https://doi.org/10.5281/zenodo.3862792) or from the shared data library > > ``` -> https://zenodo.org/record/3270536/files/SRR891268_R1.fastq.gz -> https://zenodo.org/record/3270536/files/SRR891268_R2.fastq.gz -> https://www.encodeproject.org/files/ENCFF933NTR/@@download/ENCFF933NTR.bed.gz +> https://zenodo.org/record/3862793/files/ENCFF933NTR.bed.gz +> https://zenodo.org/record/3862793/files/SRR891268_chr22_enriched_R1.fastq.gz +> https://zenodo.org/record/3862793/files/SRR891268_chr22_enriched_R2.fastq.gz > ``` > > {% include snippets/import_via_link.md %}