How To Find Comprehensive List Of Rrna Locations For C. Elegans?
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9.2 years ago
Dan D 7.3k

I've been tasked with trying to estimate how much of a sequence will align to known ribosomal RNA sequences. My current strategy is to create a ribosomal RNA intervals BED file and use that for Picard's CollectRnaSeqMetrics tool. I've actually Ribosomal Intervals For Collectrnaseqmetrics, but in this case I'm looking for C. elegans ribosomal RNA data.

If I can find any kind of data about what locations in the reference are rRNA, then I can make the BED file based on that. I've looked on the UCSC table browser, but I haven't found anything there. I also looked through the Illumina iGenomes FTP. I see in WormBook that the regions are known, but I don't see any specifics.

Does anyone know of any resources where I can find this information?

rrna bed • 6.3k views
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9.2 years ago
epistatic ▴ 190

http://genome.ucsc.edu/cgi-bin/hgTables

group: all tables database: ce6 table: rmsk filter: repClass = rRNA output format: GTF

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Do I know you? ;)

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For future readers: Epistatic is a coworker of mine. He tracked down the original paper mentioned in Wormbook, and it supports the results I got using this answer.

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nice - I know the feeling, many times I meet someone we talk, then they mention who they are on Biostar - then I have to virtually "merge" the two people

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9.2 years ago

If you could get the annotated sequences in GeneBank format from any source you could then transform them into a GFF/BED file with a program like ReadSeq

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Thanks! Converting the location data between formats isn't so much the problem here, it's getting a comprehensive list of locations. But you made me realize that I did a poor job of wording my question. I'm going to edit it accordingly.

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