Question

Bed file with the snoRNA coordinates

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9.4 years ago

wwarner1 ▴ 20

How can I download a bed file with the snoRNA coordinates? I tried biomart but no luck. Is there another way?

snoRNA genome gene • 2.6k views

ADD COMMENT • link updated 22 months ago by Ram 44k • written 9.4 years ago by wwarner1 ▴ 20

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Please give the folks here some context so we can help you better.

ADD REPLY • link 9.4 years ago by Ram 44k

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I'm interested in getting the coordinates all snoRNAs or of the introns harboring snoRNAs.

ADD REPLY • link 9.4 years ago by wwarner1 ▴ 20

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Have you tried UCSC genome Table browser (http://genome.ucsc.edu/cgi-bin/hgTables). Look under Gene and Gene prediction group.

ADD REPLY • link 9.4 years ago by Ashutosh Pandey 12k

score 1 · Answer 1 · 2015-05-26

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9.4 years ago

wwarner1 ▴ 20

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

ADD COMMENT • link 9.4 years ago by wwarner1 ▴ 20

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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.

ADD REPLY • link 6.8 years ago by venks ▴ 740

score 0 · Answer 2 · 2019-02-21

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 .