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How to download / Prepare Rfam 12 gff/gtf/bed (an annotation file) ?

Dear community,

I am working on Next generation sequencing data and need the gtf/fff/bed file to extract and calculate the ncRNAs from my mapped sam/bam file. So, could someone tell me how to prepare or download gff/gtf/bed file from new annotation of Rfam 12.0? I would like to have all non-coding RNA from Rfam 12.0 only. Any guidance?

However, I looked inside FTP (ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/) but no annotations, I have found.

Note: I don't need annotations from ensemble or ucsc table browser.

Thank you very much in advance for your help.

gene rna dataset assembly
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updated by Ram Ram • written by bioinforupesh2009.au • bioinforupesh2009.au

What would you intend to find in a GFF file of RNA structure? A GFF file is mainly for the case that you have hierarchical coordinates and annotation with respect to a larger reference sequence, e.g. genes and transcripts on a single genome assembly. RNA structures are found in many genomes and their structure doesn't really fit into annotation hierarchy of GFF either.

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updated by Ram Ram • written by Michael Dondrup Michael Dondrup

Sorry that i havnt explained my questions very well. Indeed, i am working on Next generation sequencing data and need the gtf/fgg file to extract and calculate the ncRNAs from my sample.

Thank you by the way.

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written by bioinforupesh2009.au • bioinforupesh2009.au

I think it might be best to run rfamscan to either search for ncRNAs de novo, or look for already available annotation for your organism in question. What is your organism?

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written by Michael Dondrup Michael Dondrup

Mouse (mmu). is my organism. I need gff to quantify the counts from my mapped sam/bam files.

Thanks Michael for your kind help

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written by bioinforupesh2009.au • bioinforupesh2009.au

Ok, so your question is, where can I get an annotation file with all known mouse ncRNA genes in GFF?

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updated by Ram Ram • written by Michael Dondrup Michael Dondrup

In the current release of Ensembl and the next one (i.e. 78) we have got the previous version of Rfam, i.e. v11.0

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written by Denise CS Denise CS

1 answer

How about this file: ftp://ftp.ensembl.org/pub/release-77/gtf/mus_musculus

Then filter the annotation by the biotype attribute.

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updated by Ram Ram • written by Michael Dondrup Michael Dondrup

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