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Where to find snRNA annotations?

I am working with some ChIP-seq data and I need to evaluate coverage of snRNA genes. Currently I have a BED file of all noncoding-RNA genes. Where can I find a list of snRNA genes to use as a filter for my noncoding-RNA genes? Or does there already exist somewhere an annotation file of just snRNAs?

EDIT: Forgot to say I am working with the hg38 genome.

annotation chip-seq
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written by goodez goodez

1 answer

I think I have found a solution, but I'm curious if anyone else would approach this differently?

I obtained a GTF file for hg38, and then used grep to find snRNA genes:

$ awk '$3=="gene"' hg38.Ens_91.gtf | grep "snRNA" | cut -f9 | cut -c10-24 > snRNA_IDs.txt

$ head snRNA_IDs.txt
ENSG00000252948
ENSG00000275405
ENSG00000275987
ENSG00000276711
ENSG00000277890
ENSG00000277927
ENSG00000278793
ENSG00000274202
ENSG00000278625
ENSG00000277374

This gives me a list of Ensembl gene IDs for snRNAs which I can then use to filter my noncoding RNA bed file.

• 1 views • link
written by goodez goodez

Here is a list of all snRNA's for human at RNACentral. You would need to extract the info you need from there.

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written by GenoMax GenoMax

Why should we just use 'gene' instead of 'exon' or 'transcript'?

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written by jli.ww • jli.ww

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