[DAS] Re: das track on contigview
Tony Cox
avc@sanger.ac.uk
Wed, 27 Nov 2002 16:13:17 +0000 (GMT)
On Wed, 27 Nov 2002, Alex Lam wrote:
Is the data correct in the LDAS SQL tables? (I mean, did the data get loaded
into the tables incorrectly or was the original data bad or is ensembl munging
it)
Tony
+>Hi developers,
+>I have an LDAS server serving out transcripts data and a DAS track on our local
+>ensembl website (version 8). Transcripts show up correctly except for every
+>transcript the first two exons on plus strand or the last 2 exons on minus
+>strand rendered as 1 continuous block. So all genes have 1 fewer exon and look
+>like as if they have a very long UTR.... :(
+>
+>I just wonder if anyone has seen this before and knows where the problem lies.
+>
+>I have attached the xml output from LDAS below. (In this case 169202433 to
+>169207936 is just one block, instead of 2 boxes with a hat connector) Any help
+>would be greatly appreciated.
+>
+>Thanks,
+>Alex
+>
+>
+><?xml version="1.0" standalone="yes"?>
+><!DOCTYPE DASGFF SYSTEM "http://www.biodas.org/dtd/dasgff.dtd">
+><DASGFF>
+><GFF version="1.01"
+>href="http://tartana/perl/das/dil_transcripts/features?segment=6%3A169200000%2C1
+>69220000">
+><SEGMENT id="6" start="169200000" stop="169220000" version="1.0">
+> <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/32"
+>label="AL513547.C6.1.3.mRNA">
+> <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
+> <METHOD id="exon">exon</METHOD>
+> <START>169207783</START>
+> <END>169207936</END>
+> <SCORE>-</SCORE>
+> <ORIENTATION>-</ORIENTATION>
+> <PHASE>0</PHASE>
+> <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
+> </FEATURE>
+> <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/31"
+>label="AL513547.C6.1.3.mRNA">
+> <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
+> <METHOD id="exon">exon</METHOD>
+> <START>169211105</START>
+> <END>169211254</END>
+> <SCORE>-</SCORE>
+> <ORIENTATION>-</ORIENTATION>
+> <PHASE>0</PHASE>
+> <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
+> </FEATURE>
+> <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/30"
+>label="AL513547.C6.1.3.mRNA">
+> <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
+> <METHOD id="exon">exon</METHOD>
+> <START>169211352</START>
+> <END>169211485</END>
+> <SCORE>-</SCORE>
+> <ORIENTATION>-</ORIENTATION>
+> <PHASE>0</PHASE>
+> <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
+> </FEATURE>
+> <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/29"
+>label="AL513547.C6.1.3.mRNA">
+> <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
+> <METHOD id="exon">exon</METHOD>
+> <START>169213220</START>
+> <END>169213303</END>
+> <SCORE>-</SCORE>
+> <ORIENTATION>-</ORIENTATION>
+> <PHASE>0</PHASE>
+> <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
+> </FEATURE>
+> <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/28"
+>label="AL513547.C6.1.3.mRNA">
+> <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
+> <METHOD id="exon">exon</METHOD>
+> <START>169214185</START>
+> <END>169214315</END>
+> <SCORE>-</SCORE>
+> <ORIENTATION>-</ORIENTATION>
+> <PHASE>0</PHASE>
+> <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
+> </FEATURE>
+> <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/27"
+>label="AL513547.C6.1.3.mRNA">
+> <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
+> <METHOD id="exon">exon</METHOD>
+> <START>169216402</START>
+> <END>169216508</END>
+> <SCORE>-</SCORE>
+> <ORIENTATION>-</ORIENTATION>
+> <PHASE>0</PHASE>
+> <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
+> </FEATURE>
+> <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/26"
+>label="AL513547.C6.1.3.mRNA">
+> <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
+> <METHOD id="exon">exon</METHOD>
+> <START>169219242</START>
+> <END>169219402</END>
+> <SCORE>-</SCORE>
+> <ORIENTATION>-</ORIENTATION>
+> <PHASE>0</PHASE>
+> <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
+> </FEATURE>
+> <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/33"
+>label="AL513547.C6.1.3.mRNA">
+> <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
+> <METHOD id="exon">exon</METHOD>
+> <START>169202433</START>
+> <END>169205788</END>
+> <SCORE>-</SCORE>
+> <ORIENTATION>-</ORIENTATION>
+> <PHASE>0</PHASE>
+> <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
+> </FEATURE>
+> <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/25"
+>label="AL513547.C6.1.3.mRNA">
+> <TYPE id="transcript:curated"
+>category="transcription">transcript:curated</TYPE>
+> <METHOD id="transcript">transcript</METHOD>
+> <START>169202433</START>
+> <END>169219402</END>
+> <SCORE>-</SCORE>
+> <ORIENTATION>-</ORIENTATION>
+> <PHASE>0</PHASE>
+> <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
+> </FEATURE>
+>
+></SEGMENT>
+></GFF>
+></DASGFF>
+>
+>----
+>Alex C. Lam
+>Computer Associate
+>JDRF/WT Diabetes and Inflammation Laboratory
+>Cambridge Institute for Medical Research
+>Wellcome Trust/MRC Building
+>University of Cambridge
+>Hills Road, Cambridge, CB2 2XY
+>Great Britain
+>
+>Office: 01223 763229
+>Web: http://www-gene.cimr.cam.ac.uk/todd/
+>
******************************************************
Tony Cox Email:avc@sanger.ac.uk
Sanger Institute WWW:www.sanger.ac.uk
Wellcome Trust Genome Campus Webmaster
Hinxton Tel: +44 1223 834244
Cambs. CB10 1SA Fax: +44 1223 494919
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