Myrna new reference jar

[middlemale]

I am trying to analyse rna-seq data with new Myrna tool locally, which mainly aims to compare the expression differences between control and treated samples.

The question is my species is Danio rerio and I cannot figure out how to produce reference Jar file. 'Building a reference jar using automatic scripts' in that manual sounds exclude Danio rerio.

has anyone successfully built up new reference jar file? many thanks.

[[email protected]]

same troubles...

Hi All,
I have the same problem, I need to build a custom reference jar for my organism that it is not listed in ensembl database. Do you have any idea how to do it? any manual around that can explain me how to make a working ivals directory with my custom genome? I tried analyzing all the files in a downloaded yeast jar file, and make new files with my organism annotation but without success so far.. any help would be really appreciated!
Thanks
Andrea

[Gus]

I have been trying to modify the Ensembl.pl/Ensembl.R scripts to allow creation of jars (or at least the full "ivals" directory) for arbitrary genomes but continue to run in to problems based partially on the original scripts' assumptions (every genome will have at least one exon labeled as "constitutive" and others) and random problems due to me being a python/perl guy and not too familiar with doing more than ANOVAs and the like with the R language.

I have gotten all of the ival data to be written except for the gene-footprint directories (ui,un,un_const).

These are always empty which causes the perl script to choke and of course renders myrna completely useless.

I am "THIS" close to writing this from scratch in python with pyCogent to access the Ensembl data but I can't actually find a precise description of the correct content and structure of the footprint directories/files anywhere on the myrna website.

Can ANYONE help with this?