Source of ribosomal RNA sequences to build rrna_genome index for the HTSeqGenie package
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@thomas-sandmann-6817
Last seen 9 months ago
USA

Hi Jens, hi Greg,

I would like to provide a gsnap genome index to detect ribosomal RNAs via the 'detectRRNA.rrna' config parameter of your awesome HTSeqGenie package. I couldn't find any details on how to generate a suitable index of ribosomal RNAs in the package documentation, though. (The unit test "test.detectRRNA" uses the TP53Genome() but not real rRNA data.)

For example, do you provide a set of rRNA transcript sequences (e.g. extracted from a TxDb object or a GTF file with gene annotations) and build an index from those sequences? Or is there an even better source for rRNA sequences, given that not all of the rRNA sequences may be annotated in the current reference genome?

Thanks a lot for any pointers and for providing such great tools to the community!

Thomas

HTSeqGenie • 735 views
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Jens Reeder ▴ 40
@jens-reeder-6717
Last seen 5.4 years ago

Hi Thomas,

thanks for the praise.

You should be able to pull a list from the ensembl biomart using a query like this:

(In case this link  doesn't survive pasting, it basically selects all genes with biotype rRNA and reduces to just the ones having an EntrezID)

Good luck with your analysis.

Jens

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