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| author | Pjotr Prins | 2020-05-29 11:00:08 -0500 |
|---|---|---|
| committer | Pjotr Prins | 2020-05-29 11:00:08 -0500 |
| commit | 92fa550c6edfeb9acc9a5cbc31c0c272f8703898 (patch) | |
| tree | bd2ade8b9331a3ec0211d2af99d0bd39f1a4ed7d /doc/blog/using-covid-19-pubseq-part3.html | |
| parent | 50a9933a997e468db3343023a580308b28edc653 (diff) | |
| download | bh20-seq-resource-92fa550c6edfeb9acc9a5cbc31c0c272f8703898.tar.gz bh20-seq-resource-92fa550c6edfeb9acc9a5cbc31c0c272f8703898.tar.lz bh20-seq-resource-92fa550c6edfeb9acc9a5cbc31c0c272f8703898.zip | |
Blog stuff
Diffstat (limited to 'doc/blog/using-covid-19-pubseq-part3.html')
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part3.html | 44 |
1 files changed, 36 insertions, 8 deletions
diff --git a/doc/blog/using-covid-19-pubseq-part3.html b/doc/blog/using-covid-19-pubseq-part3.html index ac32717..7903791 100644 --- a/doc/blog/using-covid-19-pubseq-part3.html +++ b/doc/blog/using-covid-19-pubseq-part3.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <head> -<!-- 2020-05-27 Wed 07:41 --> +<!-- 2020-05-29 Fri 10:00 --> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <title>COVID-19 PubSeq Uploading Data (part 3)</title> @@ -248,14 +248,16 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#org074cf76">1. Uploading Data</a></li> -<li><a href="#org00e6dd5">2. What does this mean?</a></li> +<li><a href="#orgbfd8594">1. Uploading Data</a></li> +<li><a href="#org3243122">2. Introduction</a></li> +<li><a href="#orgc7011c9">3. Step 1: Sequence</a></li> +<li><a href="#org83d22ff">4. Step 2: Metadata</a></li> </ul> </div> </div> -<div id="outline-container-org074cf76" class="outline-2"> -<h2 id="org074cf76"><span class="section-number-2">1</span> Uploading Data</h2> +<div id="outline-container-orgbfd8594" class="outline-2"> +<h2 id="orgbfd8594"><span class="section-number-2">1</span> Uploading Data</h2> <div class="outline-text-2" id="text-1"> <p> <i>Work in progress!</i> @@ -263,12 +265,38 @@ for the JavaScript code in this tag. </div> </div> -<div id="outline-container-org00e6dd5" class="outline-2"> -<h2 id="org00e6dd5"><span class="section-number-2">2</span> What does this mean?</h2> +<div id="outline-container-org3243122" class="outline-2"> +<h2 id="org3243122"><span class="section-number-2">2</span> Introduction</h2> +<div class="outline-text-2" id="text-2"> +<p> +The COVID-19 PubSeq allows you to upload your SARS-Cov-2 strains to a +public resource for global comparisons. Compute it triggered on +upload. Read the <a href="./about">ABOUT</a> page for more information. +</p> +</div> +</div> + +<div id="outline-container-orgc7011c9" class="outline-2"> +<h2 id="orgc7011c9"><span class="section-number-2">3</span> Step 1: Sequence</h2> +<div class="outline-text-2" id="text-3"> +<p> +We start with an assembled or mapped sequence in FASTA format. The +PubSeq uploader contains a <a href="https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/qc_fasta.py">QC step</a> which checks whether it is a likely +SARS-CoV-2 sequence. While PubSeq deduplicates sequences and never +overwrites metadata it probably pays to check whether your data +already is in the system by querying some metadata as described in +<a href="./blog?id=using-covid-19-pubseq-part1">Query metadata with SPARQL</a>. +</p> +</div> +</div> + + +<div id="outline-container-org83d22ff" class="outline-2"> +<h2 id="org83d22ff"><span class="section-number-2">4</span> Step 2: Metadata</h2> </div> </div> <div id="postamble" class="status"> -<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-05-27 Wed 07:41</small>. +<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-05-29 Fri 10:00</small>. </div> </body> </html> |