Build Ensembl genome index specific to long non coding RNA

Question

[shg018]

Can someone suggest a good site to get the gtf and fasta file format specific to long non coding RNA. I used http://www.gencodegenes.org/mouse_releases/current.html and its giving me errors in calculating reads with my raw read-files after mapping with the genome built using the files at this site.

[natasha.sernova]

This old post may be helpful.

Non-Annotated Long Noncoding Rna Candidates

These two below are recent:

Database for Non Coding RNA

GTF/GFF for non-coding RNA

You may find more useful posts on the right panel.