I'm trying to use Cummerbund in Galaxy, but it gives the option of "use backend database from history" or "build backend database using CuffDiff output." I've tried googling it, but I can't figure out: what is a backend database here? Does one need to be built to use Cummerbund?
-
Last edited by skmotay; 10-14-2014, 08:10 AM. -
One of the principle benefits of using cummeRbund is that data are stored in a SQLite database. This allows for out-of-memory analysis of data, quick retrieval, and only a one-time cost to setup the tables. By default, cummeRbund assumes that all output files from cuffdiff are in the current working directory. To read these files, populate the 'cuffData.db' database backend, and return the CuffSet pointer object, you can do the following.
> library(cummeRbund)
> cuff<-readCufflinks()
> cuff -
I saw that from the manual. So the database backend is just all of the files put together?Comment
-
The backend database is a database built from all the files.
I don't use Galaxy, but I have used cummeRbund directly extensively.
I assume the question is whether you want to use the database previously built or rebuild one.
Generally, you don't need to rebuild the database.
Building the database takes time.
By default, cummeRbund only builds the database once, the first time it is run.
If however, you have rerun Cuffdiff, you'll want to regenerate the database to squash the older one. Otherwise, the database used by cummeRbund will continue to be the one generated with the older run of Cuffdiff.
When you are running cummeRbund, you sometimes have to delete the older cummeRbund database to ensure that cummeRbund builds a new one, based on the most recent Cuffdiff run.Last edited by blancha; 10-14-2014, 11:44 AM.Comment
-
-
Since you appear to be using a custom build of galaxy (that has these additional tools) we can't directly help in terms of what options you are seeing on your screen. You basically want all the files from cuffdiff available and be able to point to them when you are trying to run cummeRbund. Talk to your local galaxy admin, if you are not able to figure this out.Comment
-
I think I was mostly lost on the vocabulary. Got it now.Originally posted by GenoMax View PostComment
-
hi blancha,
you say I don't have to rebuild the database. However I get an error message when trying to access the database (via the pointer object "cuff") after reloading it:
"Error in sqliteExecStatement(con,statement, bind.data): RS-DBI driver: (expired SQLiteConnection)"
Can anyone help me, how to re-establish the SQL-connection?
Sorry, I'm very new to all this...
Thanks in advanceComment
-
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment