User: mauede@alice.it

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Posts by mauede@alice.it

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is there a 1:1 correspondence between ENST and 3'UTR sequence ?
... 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 tele ...
written 7.4 years ago by mauede@alice.it850 • updated 7.4 years ago by Steffen500
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R: R: why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?
... -----Messaggio originale----- Da: seandavi@gmail.com per conto di Sean Davis Inviato: lun 31/05/2010 23.47 A: mauede@alice.it Cc: Steffen Durinck; michael watson (IAH-C); Stefano Rovetta; Giuseppe Russo; Bioconductor List Oggetto: Re: [BioC] R: why biomaRt cannot extract 3UTR sequences for 1941 EN ...
biomart written 7.5 years ago by mauede@alice.it850
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Answer: A: R: why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?
... I reinstalled all Bioconductor packages. I ran again my R script aimed at extracting 3UTR sequences of validated gene-targets. Back to "hsa-mir-1" gene-targets ... I perfoemed the following verifications and testsS: > is.list(genes_map) [1] TRUE > is.vector(genes_map[,"ensembl_transcript_id"] ...
written 7.5 years ago by mauede@alice.it850
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is database RefSeq achievable from any Bioconductor package
... The Biologist we work with has brought my attention to some misalignment between Ensembl and RefSeq with regard to the length and position of 3UTR sequences. I have been querying Ensembl many times through biomaRt . I wonder whether I can reach RefSeq data through biomaRt or any other Biconductor ...
biomart written 7.5 years ago by mauede@alice.it850
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after updating biomaRt cannot connect any more
... I recently updated R 2.10.1 Patched (2010-02-20 r51163) This morning I reinstalled biomaRt using biocLite. Now I can no more connect to biomaRt and even the following instruction is hanging for a while until the same error message pops up. > listMarts() Error in value[[3L]](cond) : Request to ...
biomart written 7.5 years ago by mauede@alice.it850 • updated 7.5 years ago by Sean Davis21k
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Answer: A: R: why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?
... This morning I have updated biomaRt (through biocLite()) as adviced. But now I cannot even connect: > hmart <- useMart('ensembl', dataset='hsapiens_gene_ensembl') is hanging ... Any idea ? Thank you, Maura -----Messaggio originale----- Da: Steffen Durinck [mailto:sdurinck@lbl.gov] Inviat ...
written 7.5 years ago by mauede@alice.it850
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R: why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?
... Those instructions worked fine in many other 3UTR extractions that requested a smaller number of ENSTzzzz I would be surprised if the query vector length were a problem. A few months ago I was suggested to download big amounts of data through one query only and then parse the output locally. Recent ...
biomart written 7.5 years ago by mauede@alice.it850
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R: why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?
... Actually, the same query has worked with a smaller number of ENST...many times for me too. But if the length of the filtering vector is really the problem then I feel confused. Some months ago I was extracting one UTR sequence at a time, thus keeping the connection to biomaRt opened for seve ...
biomart written 7.5 years ago by mauede@alice.it850 • updated 7.5 years ago by Sean Davis21k
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why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?
... I executed the following lines several times from a script as well as pasting them in an R shell. Systematically biomaRt is failing. The problem is to extract the 3UTR sequences corresponding to a vector containing 1941 Ensembl Transcript numbers (some are duplicated ... is this s problem ?) Please, ...
biomart written 7.5 years ago by mauede@alice.it850 • updated 7.5 years ago by michael watson IAH-C3.4k
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R: R: Redirection of Silencing Targets by Adenosine-to-Inosine Editing of miRNAs
... Sure. Maybe it's something that is clear to a biologist and I (as a physicist) cannot read in-between the lines. I redirected my question to a biologist at the Temple University whom we collaborate with. ... In fact I proposed to leave those miRNAs out of the validation table we are building. He dis ...
process written 7.5 years ago by mauede@alice.it850 • updated 7.5 years ago by Sean Davis21k

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