Rhoda, Thank you for the feedback, very helpful. The Gene Type filter, 'protein_coding' will likely work, however it doesn't allow me to do an 'exclude' type filter (i.e. give me everything except for the non protein-coding genes). Do you know if you can still do an exclude using the method you described?
Thank you! Phillipe ________________________________ From: Rhoda Kinsella <[email protected]> To: pip pipster <[email protected]> Cc: "[email protected]" <[email protected]> Sent: Monday, August 22, 2011 5:04 AM Subject: Re: [BioMart Users] Bug or User error with filtering? Hi Phillipe You are filtering using the protein ID (Genbank protein accession) and as this Ensembl protein ID does not have a corresponding Genbank protein accession, you will not get this ENSP. Please filter using the Gene type filter and select protein_coding. That way you will get the ENSP data you require. Regards Rhoda On 21 Aug 2011, at 22:54, pip pipster wrote: We are seeing strange things occur with the protein ID filter. For example, transcript ENST00000345514 is being filtered out by the following search below. However, you can see that it indeed has a Preotin ID shown here: http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000127152;r=14:99635624-99737861;t=ENST00000345514 . Any idea why this is being filtered? Could this be a bug in Biomart/Data or User Error? > >Manual (non-Perl) > Homo sapiens genes (GRCh37.p3) > Filters > with protein ID(s): Only > Attributes > Ensembl Gene ID > Ensembl Transcript ID > > >Same problem occurs using Perl filter as well > $query->addFilter("with_protein_id", ["Only"]); > > >Thank you, >Phillipe >_______________________________________________ >Users mailing list >[email protected] >https://lists.biomart.org/mailman/listinfo/users > Rhoda Kinsella Ph.D. Ensembl Bioinformatician, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK.
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