Re: [galaxy-user] non-coding RNA annotation

2013-09-23 Thread Jennifer Jackson 

Hello,

If you are using the Tuxedo suite of tools, then iGenomes is one good 
resource. The NCBI files represent RefSeq, and RefSeq includes 
non-coding transcripts.


NM_ = coding transcript with defined p_id, tss_id, gene_name
NR_ = non-coding transcript with defined tss_id, gene_name

The mm9 version of the iGenomes GTF file is already on the public Main 
Galaxy server at:

Shared Data - Data Libraries - iGenomes

More about the source is here, and is also where you can obtain mm10 
(download tar locally to your computer, then just upload the genes.gtf 
file as a dataset):

http://cufflinks.cbcb.umd.edu/igenomes.html

If using other software, you have many other good choices. Most will 
have user groups that suggested the best fit for the tool. Reviewing the 
'Gene and Gene Prediction' tracks at UCSC (http://genome.ucsc.edu) will 
give you an idea of those that contain non-coding, predicted, etc. 
transcripts. Biomart is also a great resource where Ensembl and other 
annotation in GTF or BED format can be reviewed and retrieved.


Thanks,

Jen
Galaxy team

On 9/22/13 7:45 PM, Hoang, Thanh wrote:

Hi all,
I am analyzing my small RNA sequencing data on mouse tissue. Does 
anyone know where to download annotation file for non-coding RNA?

Thanks
Thanh


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Jennifer Hillman-Jackson
http://galaxyproject.org

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[galaxy-user] non-coding RNA annotation

2013-09-22 Thread Hoang, Thanh 
Hi all,
I am analyzing my small RNA sequencing data on mouse tissue. Does anyone
know where to download annotation file for non-coding RNA?
Thanks
Thanh
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[galaxy-user] non-coding RNA

2011-09-29 Thread dongdong zhaoweiming 
Hi, I want to evaluate wherther my assembly transcripts produced by trinity is 
protein-coding or notcoding. I found two methods which are  txCdsPredict 
program from the UCSC(John R Prensner,2011) and Codon Substitution 
Frequencies,CSF(Michael F. Lin,2008). I wonder if galaxy can do this? Thanks a 
lot!
 
weimin zhao___
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