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<tt>Hello Julie,<br>
Defining a specific cutoff score is not very easy, as this is
something that varies across cell types.<br>
Since we are focused on potential binding within our predicted
regulatory elements, we picked a non strict p-value of 0.01 so
that we wouldn't miss potentially interesting sites.<br>
<br>
There is a subset of our motif features that we label as
'experimentally verified' and could potentially be of higher value
to you.<br>
This subset contains features that fully overlap with a relevant
ChIP-Seq peak.<br>
At the moment, there is no way to easily retrieve this subset in
gff format, but we'd be happy to offer this option if this seems
useful to you.<br>
<br>
Regards,<br>
Ilias<br>
</tt><br>
<div class="moz-cite-prefix">On 11/11/2019 17:11, Julie Sullivan
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:20191111171537.847EA62CEDD_DC99739B@hh-mx3.ebi.ac.uk">
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<div style="font-family:trebuchet ms,sans-serif;font-size:small"
class="gmail_default">Hello! I read the <a
href="http://www.ensembl.info/2018/10/15/new-ensembl-motif-features/"
moz-do-not-send="true">blog post</a> but have some questions
about the associated data file <a
href="http://ftp.ensembl.org/pub/release-98/regulation/homo_sapiens/MotifFeatures/Homo_sapiens.GRCh38.motif_features.gff.gz"
moz-do-not-send="true">Homo_sapiens.GRCh38.motif_features.gff.gz</a>.</div>
<div>
<div style="font-family:trebuchet
ms,sans-serif;font-size:small" class="gmail_default"><br>
</div>
<div style="font-family:trebuchet
ms,sans-serif;font-size:small" class="gmail_default">Do you
know what p-value was used in MOODS to generate motif
feature files? The MOODS docs give "<code>-p 0.0001" <font
face="verdana,sans-serif">as the example p-value, was
that what was used? <br>
</font></code></div>
<div style="font-family:trebuchet
ms,sans-serif;font-size:small" class="gmail_default"><code><br>
</code></div>
<div style="font-family:trebuchet
ms,sans-serif;font-size:small" class="gmail_default">Specifically
what I am really interested in how I can filter using the
score in the motif features GFF file. The scores seem to
range from -55 to 24 (or so) -- is there a associated
confidence range, e.g. "high confidence" = 20-24? Or a
cutoff score? If that makes sense? <br>
</div>
<div style="font-family:trebuchet
ms,sans-serif;font-size:small" class="gmail_default"><br>
</div>
<div style="font-family:trebuchet
ms,sans-serif;font-size:small" class="gmail_default"> Or
maybe you have more information as to how I can interpret
this score? I read the MOODS paper which did not describe
this score, and only linked to another paper which I do not
have access to.<br>
</div>
<div style="font-family:trebuchet
ms,sans-serif;font-size:small" class="gmail_default"><br>
</div>
<div style="font-family:trebuchet
ms,sans-serif;font-size:small" class="gmail_default">Thanks
so much! :)<br>
</div>
<div style="font-family:trebuchet
ms,sans-serif;font-size:small" class="gmail_default">Julie<br>
</div>
<div style="font-family:trebuchet
ms,sans-serif;font-size:small" class="gmail_default"><br>
</div>
<div style="font-family:trebuchet
ms,sans-serif;font-size:small" class="gmail_default"><br>
</div>
<div style="font-family:trebuchet
ms,sans-serif;font-size:small" class="gmail_default"><br>
</div>
<br>
</div>
<div><br>
</div>
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<br>
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