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cran / utr.annotation

:exclamation: This is a read-only mirror of the CRAN R package repository. utr.annotation — Annotate Variants in the Untranslated Regions
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How to annotate genomes using Ensembl version 75 (GRCh37)? #2

Open goodbai37 opened 3 months ago

goodbai37 commented 3 months ago

I am attempting to annotate genomic data based on GRCh37 using Ensembl version 75, as it is the only version suitable for my needs. However, Ensembl version 75 has differences compared to newer versions, such as lacking attributes like "3utr" and lacking filters like "transcript_gencode_basic."

Specifically, I am facing the following issues:

How can I effectively retrieve 3' UTR and 5'UTR sequences in Ensembl version 75? How should I handle the absence of attributes like "transcript_gencode_basic" in Ensembl version 75? Are there alternative methods or suggestions for performing effective genome annotation by GRCh37? I would appreciate any advice or guidance on how to address these challenges in Ensembl version 75. Thank you! image

gaborcsardi commented 3 months ago

Hi, this is a read only mirror of CRAN, please see the package authors in the DESCRIPTION file. Look for Maintainer, BugReports and URL. Thanks!