The release exporter should be able to export expression data from the cufflinks file
Since #984 data from the cufflinks file are no longer imported to the database. Most things that need the data has already been fixed (for example #985) to read it from the file instead. The exception is the release importer plug-in which still only has support for exporting data that is in the database.
It should not be that difficult to parse and extract information from the cufflinks file. We are already doing it in #985. We probably need some modification to pass on the data to the other files. We also need to make sure that data is sorted in the same order (it may be dangerous to assume that every cufflinks file is sorted in the same order). We can probably re-use the existing code for this since we already do similar things for data from the database.
A "side-effect" is that the matrix files will get the transcripts on columns and samples on rows instead of the (traditional) other way around.
If required, I think R or some other tool may be able to transpose the matrix files.