Question: is there a 1:1 correspondence between ENST and 3'UTR sequence ?
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gravatar for mauede@alice.it
9.4 years ago by
mauede@alice.it850 wrote:
It looks like there may be more than a 3UTR sequence for the same transcript that we identify through three keywords: hgnc_symbol, ensembl_gene_id, ensembl_transcript_id. It maybe caused by a bug in my script which I am testing.... or is such a weird situation real ? Thank you, Maura tutti i telefonini TIM! [[alternative HTML version deleted]]
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ADD COMMENTlink modified 9.4 years ago by Steffen500 • written 9.4 years ago by mauede@alice.it850
Answer: is there a 1:1 correspondence between ENST and 3'UTR sequence ?
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gravatar for Steffen
9.4 years ago by
Steffen500
Steffen500 wrote:
Hi Maura, I would expect to get just one 3UTR sequence for each transcript ID. Check in you script if all transcript IDs you're looking at are unique. Maybe a transcript ID is assigned to two HGNC symbols...which would result in multiple results for one transcript ID, it should output the same sequence though. Cheers, Steffen On Mon, Jun 14, 2010 at 3:04 PM, <mauede@alice.it> wrote: > It looks like there may be more than a 3UTR sequence for the same > transcript that we identify through three keywords: hgnc_symbol, > ensembl_gene_id, ensembl_transcript_id. > It maybe caused by a bug in my script which I am testing.... or is such a > weird situation real ? > Thank you, > Maura > > > > tutti i telefonini TIM! > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 9.4 years ago by Steffen500
Hi Maura Of the three IDs you list, only ensembl_transcript_id is a unique identifier for transcripts. Not all transcripts have an annotated 3' UTR Mick ________________________________________ From: bioconductor-bounces@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Steffen Durinck [sdurinck@lbl.gov] Sent: 14 June 2010 23:11 To: mauede at alice.it Cc: Bioconductor List Subject: Re: [BioC] is there a 1:1 correspondence between ENST and 3'UTR sequence ? Hi Maura, I would expect to get just one 3UTR sequence for each transcript ID. Check in you script if all transcript IDs you're looking at are unique. Maybe a transcript ID is assigned to two HGNC symbols...which would result in multiple results for one transcript ID, it should output the same sequence though. Cheers, Steffen On Mon, Jun 14, 2010 at 3:04 PM, <mauede at="" alice.it=""> wrote: > It looks like there may be more than a 3UTR sequence for the same > transcript that we identify through three keywords: hgnc_symbol, > ensembl_gene_id, ensembl_transcript_id. > It maybe caused by a bug in my script which I am testing.... or is such a > weird situation real ? > Thank you, > Maura > > > > tutti i telefonini TIM! > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 9.4 years ago by michael watson IAH-C3.4k
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