Question: How To Find Comprehensive List Of Rrna Locations For C. Elegans?
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gravatar for Dan D
6.8 years ago by
Dan D7.1k
Tennessee
Dan D7.1k wrote:

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 • 4.9k views
ADD COMMENTlink modified 6.4 years ago by Biostar ♦♦ 20 • written 6.8 years ago by Dan D7.1k
7
gravatar for epistatic
6.8 years ago by
epistatic180
Cambridge, MA
epistatic180 wrote:

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

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

ADD COMMENTlink written 6.8 years ago by epistatic180

Do I know you? ;)

ADD REPLYlink written 6.8 years ago by Dan D7.1k

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.

ADD REPLYlink written 6.8 years ago by Dan D7.1k

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

ADD REPLYlink modified 6.8 years ago • written 6.8 years ago by Istvan Albert ♦♦ 84k
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gravatar for Istvan Albert
6.8 years ago by
Istvan Albert ♦♦ 84k
University Park, USA
Istvan Albert ♦♦ 84k wrote:

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

ADD COMMENTlink modified 6.8 years ago • written 6.8 years ago by Istvan Albert ♦♦ 84k

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.

ADD REPLYlink written 6.8 years ago by Dan D7.1k
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