Commit f4fa192c authored by carlosribas's avatar carlosribas
Browse files

Fix links to use https

parent 46129a3d
......@@ -31,7 +31,7 @@
<h2>Links</h2>
<ul>
<li><a href="{{ $ctrl.expertDb.url }}" target="_blank">{{ $ctrl.expertDb.name }} homepage</a></li>
<li><a href="ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/database_mappings/">Mapping between {{ $ctrl.expertDb.name }} and RNAcentral accessions</a>
<li><a href="https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/database_mappings/">Mapping between {{ $ctrl.expertDb.name }} and RNAcentral accessions</a>
<li ng-if="$ctrl.expertDb.name === 'Vega'"><a href="http://www.gencodegenes.org/" target="_blank">GENCODE</a></li>
<span ng-repeat="database in ['FlyBase', 'GENCODE', 'LNCipedia', 'PomBase', 'TAIR', 'WormBase']">
......
......@@ -102,7 +102,7 @@ About RNAcentral
You can use a <a href="{% url 'genome-browser' %}">genome browser</a> to browse all mapped sequences,
view individual sequences in their genomic context,
or <a href="ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/genome_coordinates/">download genome coordinates</a>
or <a href="https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/genome_coordinates/">download genome coordinates</a>
in several formats.
<a href="{% url 'help-genomic-mapping' %}">More &rarr;</a>
</p>
......
......@@ -33,11 +33,11 @@ For a **large number of sequences**, one can:
* use an [example script](http://gist.github.com/AntonPetrov/177cef0a3b4799f01536) that works with the [RNAcentral API]({% url 'api-docs' %});
* download a [mapping file](ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/md5/)
* download a [mapping file](https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/md5/)
from the RNAcentral FTP site with correspondences
between [md5](http://en.wikipedia.org/wiki/MD5) values and RNAcentral ids;
* download a [mapping file](ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/)
* download a [mapping file](https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/)
with correspondences between external database identifiers and RNAcentral ids.
### What sequences are excluded from RNAcentral? <a style="cursor: pointer" id="excluded-sequences" ng-click="scrollTo('excluded-sequences')" name="excluded-sequences" class="text-muted smaller"><i class="fa fa-link"></i></a>
......
......@@ -12,4 +12,4 @@ in their genomic context using a light-weight **genome browser** powered by [Gen
[Ensembl Genomes](http://ensemblgenomes.org), and [UCSC genome browser](http://genome.ucsc.edu/).
The genomic coordinates of the RNAcentral entries can be **downloaded** in BED format
from the [FTP site](ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/genome_coordinates/) or through the [REST API](http://rnacentral.org/api#v1-genome-annotations).
from the [FTP site](https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/genome_coordinates/) or through the [REST API](http://rnacentral.org/api#v1-genome-annotations).
......@@ -90,10 +90,10 @@ If you need to perform a **large-scale mapping** between RNAcentral identifiers
please use the mapping files found in FTP archive:
* Mapping between RNAcentral sequences and all Expert Databases in a **single file**:
[ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/](ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/)
[https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/](https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/)
* Mapping between RNAcentral sequences and each Expert Databases in **separate files**:
[ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/database_mappings/](ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/database_mappings/)
[https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/database_mappings/](https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/database_mappings/)
---
......
......@@ -111,7 +111,7 @@ If you need to export more sequences, you can use the following workflow:
1. Download the following RNAcentral FASTA file:
[http://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/sequences/rnacentral_species_specific_ids.fasta.gz](http://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/sequences/rnacentral_species_specific_ids.fasta.gz)
[https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/sequences/rnacentral_species_specific_ids.fasta.gz](https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/sequences/rnacentral_species_specific_ids.fasta.gz)
1. Extract the sequences using [seqkit](https://bioinf.shenwei.me/seqkit/):
......
......@@ -31,7 +31,7 @@ Downloads
<h2>FTP Archive</h2>
{% with rnacentral_ftp_url='http://ftp.ebi.ac.uk/pub/databases/RNAcentral' %}
{% with rnacentral_ftp_url='https://ftp.ebi.ac.uk/pub/databases/RNAcentral' %}
<p>
To retrieve <strong>large amounts of data</strong> or to download <strong>archived data snapshots</strong>,
it is recommended to use the RNAcentral FTP Archive
......
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