Hi Jiyuan, The display of exon's start and end coordinates is back again :) The order of start and end pairs can be determined using corresponding 'rank' values [Attribute : Exon Rank in Transcript].
Kind Regards Syed On Tue, 2007-02-13 at 22:57 +1100, Jiyuan An wrote: > Hello all, > > If there are more than one exon, in the old version the header of gene > would be like |XXX,XXX,XXX|XXX,XXX,XXX|. But current version only show > |XXX|XXX|. > > > > I did as follow: > > (1) I select caenorhabdities elegans genes(CEL160) in Dataset > > (2) click Attributes (Features) --> click radio button Sequences > > --->click SEQUENCES --> click cDNA sequences --> click header > > --->information > > --> I tick chromosome, ensemble gene ID, description, ensemble > > --> transcript id, > > biotype, start position, end positon, ensemble CDS length, 5UTR start, 5UTR > end, 3UTR start, 3UTR end, exon start and exon end. > > > > Then I click button result. I give one gene to show the errors: > > > > >I|Y95B8A.6|Y95B8A.6a.2.1|882920|889792|594|882920|883166|||882920|88316 > > >I|6|protein_coding| > > >From NCBI there are 3 blocks of 5'UTR and 4 blocks of CDS. > > But in you result: only one block of 5'UTR is given |882920|883166|. > > The length is only 247, but the length of 5'UTR should be 486!. > > The length of CDS is 594, but you just give one block |882920|883166|, it > Obviously totally wrong, it's a block of 5'UTR! I used ensemble Half year > ago, it was correct. > > > > Regards, > > JiyuanAn > > > > > > > > > > > > > I have a similar problem. > > > > > > The old version (half year ago) was quiet good to download gene data. > > > but current version > > > > > > Got several errors when I download gene data from bioMart: > > > > > > 1. when a gene has several exons, only one exon's start and end (chr > > > bp) can be obtained. > > > > do you mean on the FASTA sequence header? From the structure attribute page > you can still get all the exons but there is a problem with the FASTA header > attributes that we need to fix > > > > > 2. outputted transcript attributes are wrong position. > > > > > > > again - is this on teh FASTA header? I will investigate > > > > best wishes > > Damian > > > > > > > > > > > > > > > _____ > > > > > > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On > > > Behalf Of Maratou, Klio > > > Sent: Monday, 12 February 2007 10:18 PM > > > To: [email protected] > > > Subject: [mart-dev] FW: query output inconsistency > > > > > > > > > > > > > > > > > > > > > > > > Klio Maratou, PhD > > > > > > MRC Clinical Sciences Centre > > > > > > Imperial College School of Medicine > > > > > > Hammersmith Hospital > > > > > > Du Cane Road > > > > > > London, W12 ONN > > > > > > Email:[EMAIL PROTECTED] > > > > > > Tel: 020 8383 4319 > > > Fax: 020 8383 8577 > > > > > > > > > > > > _____ > > > > > > From: Maratou, Klio > > > Sent: Mon 12/02/2007 11:00 > > > To: [EMAIL PROTECTED] > > > Subject: query output inconsistency > > > > > > I have a question about an inconsistency that I found when I query the > > > biomart Rattus norvegicus genes (RGSC3.4) dataset. If under Filters I > > > use the chromosome number along with base start and end positions to > > > query biomart, then I get a specific number of genes that are in this > > > genomic interval. However, if I repeat this query using marker names > > > for start and end, then I get a different number of genes for the same > genomic interval. > > > The sequence start and end positions that I use are based on the > > > sequence positions of the markers. > > > > > > Why is there a difference in the output? > > > > > > Best wishes, > > > > > > Klio Maratou > > > > > > > > > > > > Klio Maratou, PhD > > > > > > MRC Clinical Sciences Centre > > > > > > Imperial College School of Medicine > > > > > > Hammersmith Hospital > > > > > > Du Cane Road > > > > > > London, W12 ONN > > > > > > Email:[EMAIL PROTECTED] > > > > > > Tel: 020 8383 4319 > > > Fax: 020 8383 8577 > > > > > > > > > > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
