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Small update in ATAC-Seq training material #1903

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May 28, 2020
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Small update in ATAC-Seq training material #1903

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4231378
update zenodo
lldelisle May 28, 2020
011327d
update zenodo link and create data-library.yaml
lldelisle May 28, 2020
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29 changes: 29 additions & 0 deletions topics/epigenetics/tutorials/atac-seq/data-library.yaml
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Original file line number Diff line number Diff line change
@@ -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
10 changes: 5 additions & 5 deletions topics/epigenetics/tutorials/atac-seq/tutorial.md
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Expand Up @@ -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?
Expand Down Expand Up @@ -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 %}
Expand Down