[ensembl-dev] motif features - what's a "good" score?
Ilias Lavidas
ilavidas at ebi.ac.uk
Tue Nov 12 13:16:41 GMT 2019
Hello Julie,
Defining a specific cutoff score is not very easy, as this is something
that varies across cell types.
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.
There is a subset of our motif features that we label as 'experimentally
verified' and could potentially be of higher value to you.
This subset contains features that fully overlap with a relevant
ChIP-Seq peak.
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.
Regards,
Ilias
On 11/11/2019 17:11, Julie Sullivan wrote:
> Hello! I read the blog post
> <http://www.ensembl.info/2018/10/15/new-ensembl-motif-features/> but
> have some questions about the associated data file
> Homo_sapiens.GRCh38.motif_features.gff.gz
> <http://ftp.ensembl.org/pub/release-98/regulation/homo_sapiens/MotifFeatures/Homo_sapiens.GRCh38.motif_features.gff.gz>.
>
> Do you know what p-value was used in MOODS to generate motif feature
> files? The MOODS docs give "|-p 0.0001" as the example p-value, was
> that what was used?
> |
> |
> |
> 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?
>
> 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.
>
> Thanks so much! :)
> Julie
>
>
>
>
>
>
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