Question

Where Can I Download Lincrna Feature Files For The Mm9 Genome Build

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11.5 years ago

Zev.Kronenberg 12k

Does anyone know where I can get a valid mm9 gtf or gff3 lincRNA dataset? I need relationship data within these files.

So far my searching has lead me to believe that only coordinate files exist. The only feature type I have found is 'exon'

Thank you very much!

-I am one desperate dude.

gtf gff • 4.3k views

ADD COMMENT • link updated 11.5 years ago by JC 13k • written 11.5 years ago by Zev.Kronenberg 12k

score 2 · Answer 1 · 2012-10-12

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11.5 years ago

JC 13k

subtract the lincRNA from the Ensembl annotation:

wget ftp://ftp.ensembl.org/pub/release-68/gtf/mus_musculus/Mus_musculus.GRCm38.68.gtf.gz
zgrep lincRNA Mus_musculus.GRCm38.68.gtf.gz > lincRNA.gtf

*the last mouse assembly is mm10, I'm almost sure that Ensembl is using that annotation, if you need mm9 maybe you will need to search in previous releases.

ADD COMMENT • link 11.5 years ago by JC 13k

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Yes this annotation is much better! However, there are way fewer lincRNAs than I have seen in other sets.

ADD REPLY • link 11.5 years ago by Zev.Kronenberg 12k

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yes, but consider that lincRNA biology is still in research. Recently I take a look of the lincRNAs printed in a human microarray, many probes were bad, some marks introns and others are alternative transcripts from a large coding gene. Be careful with annotations.

ADD REPLY • link 11.5 years ago by JC 13k

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The quality of the annotations has been bothering me since I have started looking into lincRNAs.

ADD REPLY • link 11.5 years ago by Zev.Kronenberg 12k