User: Victoria Perreau

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1 month, 2 weeks ago
Joined:
12 years, 9 months ago
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v*******@unimelb.edu.au

Posts by Victoria Perreau

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Trying to map nucleotide position from a transcript to genomic location
... Using the UCSC genome browser and the blat tool to close in on the region of interest, I have manually mapped the genomic location I would expect for transcript position 1409 for two transcripts from the Bcap29 gene. These locations correspond to genome version mm10. Position 1409 in transcript NM_ ...
written 6 weeks ago by Victoria Perreau20
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Comment: C: Trying to map nucleotide position from a transcript to genomic location
... Hi Valerie, thank you for your detailed response. I agree with you that the 3'UTRs and 5'UTRs of the gene are mapped correctly to the genome.  However, when I map the genome coordinate mm10, chr12:31633250, that was returned for the nucleotide position 1409 of transcript for gene "Bcap29", it does ...
written 7 weeks ago by Victoria Perreau20
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Comment: C: Trying to map nucleotide position from a transcript to genomic location
... I have since found a solution to the mapping problem using the package "ensembldb" following the tutorial at the link below. https://bioconductor.org/packages/devel/bioc/vignettes/ensembldb/inst/doc/coordinate-mapping.html#6_mapping_transcript_coordinates_to_genomic_coordinates   ...
written 8 weeks ago by Victoria Perreau20
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Comment: C: Trying to map nucleotide position from a transcript to genomic location
... Hi James, thank you for your answer. I want to map based on the position that the mature miRNA binds to a gene transcript.  This is often in the 3'UTR of a transcript. The position is the nucleotide number based on the beginning of the transcript and not a genomic location.  However I should be abl ...
written 8 weeks ago by Victoria Perreau20
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Trying to map nucleotide position from a transcript to genomic location
... I am trying to obtain genomic locations corresponding to predicted miRNA binding sites on transcripts, in order to construct a bedfile for visualizing these binding sites in the UCSC genome browser.  The location data I have for miRNA binding sites is the nucleotide position in the mRNA obtained fro ...
mirna genomicfeatures mapfromtranscripts written 8 weeks ago by Victoria Perreau20 • updated 8 weeks ago by Valerie Obenchain ♦♦ 6.6k
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MG_U74A version 1 sequence info
... I am trying to reanalyse some older data and would like to be able to make a custom cdf to the old Mg_u74a chip. I have the original cdf file but cant get hold of the v1 probe sequence file (if it was ever available). I am aware of all the issues with this particular chip and though that some of t ...
cdf probe written 12.8 years ago by Victoria Perreau20

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