Question: Ribosomal Intervals For Collectrnaseqmetrics
4
gravatar for Johan
5.6 years ago by
Johan820
Sweden
Johan820 wrote:

Does anyone know if there is some publicly available ribosomal interval list for use with CollectRnaSeqMetrics in the Picard suite? Specifically I'm looking for a interval list for the Human genome in build g1k_v37. I found a description of how to generate my own in the faq but for obvious reasons it would be nice if there is one ready to use somewhere out there. Googleing hasn't turned anything up for me this far, so I thought I'd turn to the community to ask.

picard qc rna-seq • 6.2k views
ADD COMMENTlink modified 3.9 years ago by Kamil1.8k • written 5.6 years ago by Johan820
3
gravatar for Dan D
5.5 years ago by
Dan D6.6k
Tennessee
Dan D6.6k wrote:

Hi Johan,

I was researching this exact question today and came across this post by Alec Wysoker, the author of Picard tools:

http://sourceforge.net/mailarchive/message.php?msg_id=27560147

I would just post his list here but it exceeds the character limit. I had to take out the @SQ lines referencing "GL" locations (the lines after 26), but other than that it worked great for me.

EDIT: You need to make sure your chromosome names in the @SQ lines match the first column in your interval list. I can give more detail if you don't already know what I'm talking about.

EDIT 2: Also ran across this site while searching for mouse:

http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html#download-ribosome-rna-update-to-08-17-2012

ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by Dan D6.6k

I don't know if that list is complete if you're using all the contigs. We get a lot of rRNA reads aligning to contig GL000220.1

ADD REPLYlink written 3.6 years ago by Michele Busby1.9k
1
gravatar for Kamil
3.9 years ago by
Kamil1.8k
Boston
Kamil1.8k wrote:

You can see my ribosomal intervals file and a simple script I used to create it here:

https://gist.github.com/slowkow/b11c28796508f03cdf4b

ADD COMMENTlink written 3.9 years ago by Kamil1.8k

Thank you for sharing Kamil. I made a couple of changes to the script use other species and rRNA can be in bed format: https://gist.github.com/adomingues/57e3c2f9f4aca8dfde7b

Of course, you have been acknowledged.  I hope you don't mind :)

ADD REPLYlink written 3.7 years ago by A. Domingues1.6k
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