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Old 05-17-2013, 05:14 AM   #1
hanshart
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Location: Germany

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Default ENSEMBL biotype tRNA and non-coding RNA

Hello, I have two questions concerning the ENSEMBL annotation files (GTFs for human, mouse).

1. Can anyone explain to me why there is no gene_biotype "tRNA" (but "rRNA","Mt_rRNA", "Mt_tRNA") annotated in the annotation files for human and mouse (ENSEMBL version 70), although it is documented? See http://www.ensembl.org/info/docs/genebuild/ncrna.html
Ok, GENCODE (should use the same database as ENSEMBL) does not list it -> http://www.gencodegenes.org/gencode_biotypes.html
Is tRNA described by other biotypes?

2. Does anyone know how "complete" the ENSEMBL non-coding RNA annotations are in contrast to specialized non-coding RNA databases (especially for lincRNA)? If I apply an analysis to output percentage of mapped reads per biotype based only on the ENSEMBL annotation file, whould this analysis be representative for the non-coding RNAs (for human and for mouse)?

Thank you

Last edited by hanshart; 05-17-2013 at 11:06 AM. Reason: null
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Old 12-05-2014, 02:49 AM   #2
sudders
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Default

Hi,

Did you ever get this sorted? I can't seem to find any annotation of tRNAs in human ensembl.

Ian
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