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_XXXX = coding transcript with defined p_id, tss_id, gene_name
NR_XXXX = 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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