Extract All Long Non-Coding Rna For Mouse

Question

[ancient_learner]

Hi all i was just trying to extract all the non-coding rna data for mouse from ucsc genome browser. from the table browser i got all the list of refseq genes. is it ok if i just grep those which contain NR as suffix for getting all long non coding rna? or is there any method for the same.

[Devon Ryan]

That will also contain microRNAs.

[ancient_learner]

then how can i get only long non coding rna data? please give your suggestions

[Devon Ryan]

You might download kgXref and then grep "non-coding" kgXref | cut -f 2 | sort | uniq to get a list of names and then use that with grep (microRNAs aren't labeled as non-coding in kgXref). A more convenient way would be to just add the full name of each gene to the GTF file and then grep for "non-coding" in that (it's often convenient to have a gene_name field in GTF files). I expect there are instructions elsewhere on biostars on how to do that.

Edit: Of course, this all depends on the annotations containing "non-coding" in their names, which I can't guarantee is always the case.

Edit2: If you're willing to use the Ensembl annotation then life is easier (you can even just use biomart). I would normally recommend the Ensembl annotation anyway, it's much cleaner.

Answer 1

[Ashutosh Pandey]

I found this (http://redmine.soe.ucsc.edu/forum/index.php?t=msg&goto=13211&S=eff182afb7e57f9d63444435c3804be2) on UCSC genome browser. This will also give you structural RNAs, transcribed pseudogenes along with non-coding RNA. You may set some length limit.