Warning!
please note that if you are setting up a das server with a stylesheet,
be sure to not have <BUMP>0</BUMP> as strange things happen in clients
such as ensembl- remove these tags if you're not sure what to do with
them!
Thanks
Jonathan
See issue below posted to ensembl dev list:
Abel Ureta-Vidal wrote:
Hi,
This is maybe more for the DAS/Web team. I'm interested in
structural variation data (CNV, chromosome gain/loss, etc....)
I've identified some data in Ensembl that is integrated via DAS
sources. I've identified the original DAS sources and
query them directly, no problem, they work as expected.
I'd just like to report a couple of things on the Ensembl web
display side of things.
1/The live ensembl server points to 2 DAS sources for CNVs from
Redon et al paper (Nature 2006 I presume),
i.e. WGTP_loci_36 and WGTP_regions_36.
I could not find a clear description of the exact difference between
the 2, (what does WGTP stands for? Whole Genome
Tiling Platform?). Querying them directly and looking at their data,
it seems that these are 2 identical data sets
$ GET http://das.sanger.ac.uk/das/WGTP_loci_36/features?segment=5:17198060,18198059
> WGTP_loci_36
$ GET http://das.sanger.ac.uk/das/WGTP_regions_36/features?segment=5:17198060,18198059
> WGTP_regions_36
$ diff WGTP_loci_36 WGTP_regions_36
5c5
< <GFF version="1.01" href="http://das.sanger.ac.uk:80/das/WGTP_loci_36/features
">
---
> <GFF version="1.01" href="http://das.sanger.ac.uk:80/das/WGTP_regions_36/features
">
If I query the complete data from chromosome 5, I get exactly the
same **none** difference. These 2 sources
seem to be identical. Only WGTP_regions_36 is listed and validate in
the DAS registry (www.dasregistry.org). Should
this one only be considered as the reference?
On the short region I queried 5:17198060,18198059, 5 features come
back. But I can only see 4 in the Ensembl Detailed View
FEATURE id="Chr5tp-4G10:Gain=32|loss=39" label="Chr5tp-4G10:Gain=32|
loss=39"
START 17417700
END 17583657
seems to be missing.
All features have different ids so this is not a feature grouping
artifact I presume.
2/ Same kind of issue with decipher and decipher_collapsed_36
sources. Only decipher is in the DAS registry.
$ GET http://das.sanger.ac.uk/das/decipher/features?segment=5:16621834,16821833
> decipher
$ GET http://das.sanger.ac.uk/das/decipher_collapsed_36/features?segment=5:16621834,16821833
> decipher_collapsed
$ diff decipher decipher_collapsed
5c5
< <GFF version="1.01" href="http://das.sanger.ac.uk:80/das/decipher/features
">
---
> <GFF version="1.01" href="http://das.sanger.ac.uk:80/das/decipher_collapsed_36/features
">
Here 4 features are returned but only 1 displayed.
So am I missing something? or these sources are data duplications.
And is there a display problem?
This is an identified issue - the DAS sources in both cases say DO NOT
BUMP - so we don't hence we cannot display all the features. We have
solved this for some sources by getting them to remove the "<BUMP>0</
BUMP>" entries in the stylesheets.
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