the _locations_ of all non-coding RNAs on chromosome 5

Question

[gy852507309]

I have already found the database of chromosome 5 on UCSC,but where to Download the _locations_ of all non-coding RNAs on chromosome 5 (in BED or GFF format)? Thank you in advanced

[Denise CS]

You can download the annotation of both ncRNA and protein coding genes from the Ensembl FTP as GTF and then get the location for those ncRNA on chromosome 5. BioMart can also be used to download the genomic location of ncRNA on chromosome 5. The output of BioMart can be tsv and cvs (among others).

Answer 1

[Michael]

Did you try Ensembl Biomart with a query like this: Biomart query

Make sure the genome build is the same as in your download from UCSC.