add chira training to rna page and a blog post

_posts/2020-03-24-rna-interactome.md

@@ -0,0 +1,11 @@
+---
+site: freiburg
+tags: [tools]
+title: ChiRA tool suite - an integrated framework for Chimeric Read Analysis from RNA-RNA interactome data
+---
+
+- ChiRA is a set of tools to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, LIGR-Seq, etc. The reads from these datasets are chimeric, i.e, two interacting RNA fragments fused into a single read. Limitations of the current library preparation protocols limit the length of each sequenced interacting RNA fragment. These smaller RNA fragments are often harder to map considering that the boundaries of each RNA fragment in the read are unknown. ChiRA tool suite maps these reads sensitively and infers the true origins of them by quantifying the mapped loci. The visualization framework ChiRAViz gives flexibility in filtering and searching output files, visualize the summaries of filtered data as well as exporting them.
+
+- You can learn the usage of the ChiRA tool suite to analyze your interactome datasets from the galaxy training material: [RNA-RNA interactome data analysis](https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/rna-interactome/tutorial.html).
+
+- ChiRA is now part of the RNA workbench ([RNA workbench](https://rna.usegalaxy.eu/)).

index-rna.md

@@ -51,6 +51,7 @@ Network analysis with Heinz <i class="fa fa-users" aria-hidden="true"></i>| [<i
 PAR-CLIP analysis |  |  | [<i class="fa fa-files-o" aria-hidden="true"></i>](http://doi.org/10.5281/zenodo.2553519){:target="_blank"} | [<i class="fa fa-share-alt" aria-hidden="true"></i>]({{ page.website }}/workflows/run?id=a108b575b16e6cb9){:target="_blank"} |  | [<i class="fa fa-list-ul" aria-hidden="true"></i>]({{ page.website }}/u/joerg-fallmann/h/parclipworkflow){:target="_blank"}
 Reference-based RNA-Seq data analysis |  | [<i class="fa fa-laptop" aria-hidden="true"></i>](https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html){:target="_blank"} | [<i class="fa fa-files-o" aria-hidden="true"></i>](https://zenodo.org/record/1185122){:target="_blank"} | [<i class="fa fa-share-alt" aria-hidden="true"></i>]({{ page.website }}/workflows/run?id=9c7a218993788493){:target="_blank"} | [<i class="fa fa-magic" aria-hidden="true"></i>]({{ page.website }}/tours/ref_based_rna-seq){:target="_blank"} | [<i class="fa fa-list-ul" aria-hidden="true"></i>]({{ page.website }}/u/andrea.bagnacani/h/reference-based-rna-seq){:target="_blank"}
 RNA family model construction |  |  |  | [<i class="fa fa-share-alt" aria-hidden="true"></i>]({{ page.website }}/workflows/run?id=8f2d958cee428ca1){:target="_blank"} |  |
+RNA-RNA interactome data analysis |  | [<i class="fa fa-laptop" aria-hidden="true"></i>](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-interactome/tutorial.html){:target="_blank"} | [<i class="fa fa-files-o" aria-hidden="true"></i>](https://zenodo.org/record/3696889){:target="_blank"} | [<i class="fa fa-share-alt" aria-hidden="true"></i>]({{ page.website }}/workflows/run?id=25a209bda998412f){:target="_blank"} |  | [<i class="fa fa-list-ul" aria-hidden="true"></i>]({{ page.website }}/u/videmp/h/rna-rna-interactome-analysis){:target="_blank"}
 RNA-seq counts to genes |  | [<i class="fa fa-laptop" aria-hidden="true"></i>](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.html){:target="_blank"} | [<i class="fa fa-files-o" aria-hidden="true"></i>](https://figshare.com/s/f5d63d8c265a05618137){:target="_blank"} | [<i class="fa fa-share-alt" aria-hidden="true"></i>]({{ page.website }}/workflows/run?id=86f89f49431b1e2e){:target="_blank"} |  | [<i class="fa fa-list-ul" aria-hidden="true"></i>]({{ page.website }}/u/videmp/h/rna-workbench-rna-seq-counts-to-genes){:target="_blank"}
 RNA-seq genes to pathways |  | [<i class="fa fa-laptop" aria-hidden="true"></i>](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.html){:target="_blank"} | [<i class="fa fa-files-o" aria-hidden="true"></i>](https://zenodo.org/record/2596382){:target="_blank"} | [<i class="fa fa-share-alt" aria-hidden="true"></i>]({{ page.website }}/workflows/run?id=3cb45f0d38e9fd42){:target="_blank"} |  | [<i class="fa fa-list-ul" aria-hidden="true"></i>]({{ page.website }}/u/videmp/h/rna-workbench-rna-seq-genes-to-pathways){:target="_blank"}
 RNA-Seq reads to counts |  | [<i class="fa fa-laptop" aria-hidden="true"></i>](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html){:target="_blank"} | [<i class="fa fa-files-o" aria-hidden="true"></i>](https://figshare.com/s/f5d63d8c265a05618137){:target="_blank"} | [<i class="fa fa-share-alt" aria-hidden="true"></i>]({{ page.website }}/workflows/run?id=e89761c4bb25d89c){:target="_blank"} |  | [<i class="fa fa-list-ul" aria-hidden="true"></i>]({{ page.website }}/u/videmp/h/rna-workbench-rna-seq-reads-to-counts-1){:target="_blank"}