Entering edit mode
10.0 years ago
bioinforupesh2009.au
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140
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.
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.
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.
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?
Mouse (mmu). is my organism. I need gff to quantify the counts from my mapped sam/bam files.
Thanks Michael for your kind help
Ok, so your question is, where can I get an annotation file with all known mouse ncRNA genes in GFF?
Indeed NO. But I would say, i can get annotation from ensemble ( http://www.ensembl.org/info/data/ftp/index.html ) or from USCS Table but i really need annotation from Rfam version 12.0 (the newest released version). this is what i need.
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