Question: ncRNA mouse file from UCSC or other source
1
gravatar for kanwarjag
5.2 years ago by
kanwarjag1.0k
United States
kanwarjag1.0k wrote:

How can I get list of all mouse ncrna with there complete annotation and coordinates. Will UCSC browser be the best source, How should I get that list 

ncrna mouse • 1.3k views
ADD COMMENTlink modified 5.2 years ago by Alex Reynolds30k • written 5.2 years ago by kanwarjag1.0k
1
gravatar for Alex Reynolds
5.2 years ago by
Alex Reynolds30k
Seattle, WA USA
Alex Reynolds30k wrote:

You can use the MySQL client:

$ mysql --user genome --host genome-mysql.cse.ucsc.edu -D mm9 -N -e  "select chrom, txStart, txEnd, name, strand from refGene WHERE name like 'NR_%'" | sort-bed - > ncRNA.mm9.bed

If you're working with mm10:

$ mysql --user genome --host genome-mysql.cse.ucsc.edu -D mm10 -N -e  "select chrom, txStart, txEnd, name, strand from refGene WHERE name like 'NR_%'" | sort-bed - > ncRNA.mm10.bed

Once you have BED files, you can use bedops or bedmap to relate ncRNAs to annotation tables from other sources.

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by Alex Reynolds30k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1257 users visited in the last hour