Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
Open sidebar
genotoul-bioinfo
ng6
Commits
1c2e19ab
Commit
1c2e19ab
authored
Apr 17, 2019
by
Maxime Manno
🍜
Browse files
Update visualisation of RunStat ONT : update help
parent
d215dd4f
Changes
1
Hide whitespace changes
Inline
Side-by-side
ui/nG6/pi1/analyzes/Run_stats.tpl
View file @
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>
Me
di
an read quality
</strong>
:
The me
di
an 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>
D
istribution
length
</strong>
:
The length distribution of reads for this Flow Cell with reads count
or bases
count.
<li><strong>
Length d
istribution
</strong>
:
The length distribution of reads for this Flow Cell with reads count count.
</li>
<li><strong>
D
istribution
qscore
</strong>
:
<li><strong>
Qscore d
istribution
</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
}
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment