Hi,
From ~28000 mm9 genes with refseq,ensembl,ucsc known id, gene symbol, and description for RNA-seq data, I am trying to get information of percentage for each group, RNA,tRNA,rRNA,snRNA, lincs. Since there are gene symbol and description for each gene, therefore, if i take a look at genes, roughly i am able to get where particular gene belongs to. But i would like to get an exact percentage how many genes belong to tRNA, how many genes to rRNA/snRNA/...etc
how can i get such information?
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written
by
Hamilton •
If you have Ensembl gene ids you can get the 'gene_biotype' for each. There are many ways to access this information from Ensembl. For example:
This GTF file contains the biotypes for 37,681 genes: ftp://ftp.ensembl.org/pub/release-64/gtf/mus_musculus/Mus_musculus.NCBIM37.64.gtf.gz
NCBI Mouse Build 37 is 'mm9' according to UCSC: http://genome.ucsc.edu/FAQ/FAQreleases.html
Each gene is classified by one of the following in this Ensembl mouse version.
IG_C_gene IG_D_gene IG_J_gene IG_V_gene Mt_rRNA Mt_tRNA lincRNA miRNA misc_RNA polymorphic_pseudogene processed_transcript protein_coding pseudogene rRNA snRNA snoRNA
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written
by
Malachi Griffith
Get your list of sequences in GenBank format, and look for ncRNA features. They should have an /ncRNA_class attribute which will tell you whether it represents tRNA, a snoRNA, etc.
True +1. One need not get the sequences in GenBank format per se, but capture the GenBank features in flatfile or similar format.
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What is mm9? Is this a build of the mouse genome?
the latest mouse genome