How can I download a bed file with the snoRNA coordinates? I tried biomart but no luck. Is there another way?
Please give the folks here some context so we can help you better.
I'm interested in getting the coordinates all snoRNAs or of the introns harboring snoRNAs.
Have you tried UCSC genome Table browser (http://genome.ucsc.edu/cgi-bin/hgTables). Look under Gene and Gene prediction group.
Thank you for your reply, Ashutosh. That gives me "sno/miRNA" as a group under track. Im trying to get the coordinates for only the snoRNAs
hi wwarner1 did you get to find the source for getting the SNORNAs bed?? I am trying to find the same since I wanted to remove exclude these regions from my BAM.
This is an older post, but for people searching through BioStar in the future, use RNAcentral for the most comprehensive database on snoRNAs or any other ncRNA type. You can download FASTA or BED or GTF files, for your species and/or RNA type. For example all human snoRNAs, https://rnacentral.org/search?q=RNA%20AND%20TAXONOMY:%229606%22%20AND%20rna_type:%22snoRNA%22 .
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