Commit 485bc0db authored by Maxime Manno's avatar Maxime Manno 🍜
Browse files

Merge branch 'nG6_ont-qc_update' into 'master'

Update visualisation of RunStat ONT : update help

See merge request !25
parents 002b5c46 1c2e19ab
......@@ -208,7 +208,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<td><label>Cumulate Yield per second</label></td>
<td><a class="imglink" href="{$plots.$head}" ><i class="glyphicon glyphicon-picture"></i></a></td>
{elseif ($head == 'distriblength')}
<td><label>Length distribution</label></td>
<td><label>Length distribution by reads</label></td>
<td><a class="imglink" href="{$plots.$head}" ><i class="glyphicon glyphicon-picture"></i></a></td>
{elseif ($head == 'distriblength_bybases')}
<td><label>Length distribution by bases</label></td>
......@@ -356,12 +356,11 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<br><br>
{/if}
{* Help block *}
{if $template_status == "2.0"}
<div class="tx-nG6-pi1-help">
<img src="" alt="" class="img" />
<p>Help for Basic metrics report :</p>
<p>Help for ONT metrics report :</p>
<span class="meta">
<ul>
<li><strong>Nb reads</strong> :
......@@ -370,15 +369,87 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<li><strong>Total bases</strong> :
The number of bases for this Flow Cell.
</li>
<li><strong>Median/Mean read length</strong> :
<li><strong>Mean read length</strong> :
The median or mean length of the total reads (bases).
</li>
<li><strong>N50 read length</strong> :
50% of all bases come from reads longer than this value.
</li>
<li><strong>Mean read quality</strong> :
The mean quality (qscore ONT) for this Flow Cell.
</li>
<li><strong>Mean yield per sec</strong> :
The mean number of bases per second for the pores of this Flow Cell.
</li>
<li><strong>Q7</strong> :
Filtered data composed by reads with quality > 7.
</li>
<li><strong>Q9</strong> :
Filtered data composed by reads with quality > 9.
</li>
</ul>
</span>
</div>
<div class="tx-nG6-pi1-help">
<img src="" alt="" class="img" />
<p>Help for Plots report :</p>
<span class="meta">
<ul>
<li><strong>Cumulate yield per second</strong> :
The cumulate number of bases per hour for this Flow Cell.
</li>
<li><strong>Length distribution</strong> :
The length distribution of reads for this Flow Cell with reads count or bases count.
</li>
<li><strong>Quality distribution</strong> :
The quality (qscore ONT) distribution of reads for this Flow Cell.
</li>
{if $barcode_name_count > 1 }
<li><strong> Qscore boxplot</strong> :
Boxplots for each barcode of the mean qscore of reads for this Flow Cell.
</li>
<li><strong> Qscore per time intervals boxplot</strong> :
Boxplots for each barcode of the mean qscore of reads per interval of time for this Flow Cell.
</li>
{/if}
</ul>
</span>
</div>
{if $barcode_name_count > 1 }
<div class="tx-nG6-pi1-help">
<img src="" alt="" class="img" />
<p>Help for Barcode ONT results :</p>
<span class="meta">
<ul>
<li><strong>Barcode score</strong> :
The quality score of the barcode alignment.
</li>
</ul>
</span>
</div>
{/if}
{else}
<div class="tx-nG6-pi1-help">
<img src="" alt="" class="img" />
<p>Help for Basic metrics report :</p>
<span class="meta">
<ul>
<li><strong>Nb reads</strong> :
The total number of reads for this Flow Cell (including the reads that are filtered during the basecalling).
</li>
<li><strong>Total bases</strong> :
The number of bases for this Flow Cell.
</li>
<li><strong>Median/mean read length</strong> :
The median or mean length of the total reads (bases).
</li>
<li><strong>N50 read length</strong> :
50% of all bases come from reads longer than this value.
</li>
<li><strong>Median yield per sec</strong> :
The median number of bases per second for the pores of this Flow Cell.
</li>
</ul>
</span>
</div>
......@@ -387,8 +458,8 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<p>Help for Quality report :</p>
<span class="meta">
<ul>
<li><strong>Mean read quality</strong> :
The mean quality (qscore ONT) for this Flow Cell.
<li><strong>Median read quality</strong> :
The median quality (qscore ONT) for this Flow Cell.
</li>
{if $template_status != "2.0"}
<li><strong>Useful data</strong> :
......@@ -396,12 +467,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
</li>
{/if}
{if $template_status == "2.0"}
<li><strong>Q7</strong> :
Filtered data composed by reads with quality > 7.
</li>
<li><strong>Q9</strong> :
Filtered data composed by reads with quality > 9.
</li>
{/if}
</ul>
</span>
......@@ -415,10 +481,10 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<li><strong>Cumulate yield per hour</strong> :
The cumulate number of bases per hour for this Flow Cell.
</li>
<li><strong>Distribution length</strong> :
The length distribution of reads for this Flow Cell with reads count or bases count.
<li><strong>Length distribution</strong> :
The length distribution of reads for this Flow Cell with reads count count.
</li>
<li><strong>Distribution qscore</strong> :
<li><strong>Qscore distribution</strong> :
The quality (qscore ONT) distribution of reads for this Flow Cell.
</li>
{if $barcode_name_count > 1 }
......@@ -445,5 +511,6 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
</span>
</div>
{/if}
{/if}
{/block}
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment