grouping of small RNA species
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4.8 years ago
HK ▴ 40

From ~22144 human 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 non-coding small RNA group (snoRNA, snRNA, scRNA, piwiRNA,micro RNA). 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 snoRNA, how many genes to snRNA...etc.

how can i get such information?

And by just looking at the ~2100 genes, how would i know which gene is for which catogory, like i know all genes starting with MIR is all microRNAs. So what about others?

small-rna rna-seq • 1.2k views
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from ensemble biomart, download the gene symbol and its biotype which gives you the result. Same thing can be found in the feature file also (gtf/gff)

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thank you prasad for the reply. But can you kindly explain a bit more how to do this. As that is something new for me.

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GO to ensemble biomart → Ensemble Genes → Select Organism → Attribute, from the attribute section select what are all the information you want. Gene_Type is the one you are looking.

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