Hi. I am a new user of the Staden package. I am using it through linux, and I encountered a few problems while trying to solve the exercise in the following link: http://www.visualgenomics.ca/MDSC675/
to start with, I couldn't use the files I created in the exercise in the original pregep and gap directories, and I had to move them to a different directory, where I had writing permission. then, following the exercise I got to a part where I need to edit my assembly (step 5 in the exercise). Double-clicking a base in a sequence should open a trace viewer window. The problem is, no such window opens, and I get a message in the command line of Gap4, saying it couldn't open the file. Basically, I'm stuck there.
Can someone tell me what went wrong?
By default, the database and the trace files (exp and ztr files) have to be in the same directory for the trace viewing to work.
If not, look at Options->Trace File Location and see what that does....
I didn't understand what database you're reffering to. is it the database I build myself or is it the database that came with the package? what directory should contain that database?
You had some trace files. You ran pregap4 on them. Then you used those to create a gap4 database and assembled them.
The pregap4 output files (exp and ztr) and the gap4 database have to be in the same directory (any directory where you have access).
You mentioned you moved files to a different directory. Move EVERYTHING there: all your exp and ztr files and also the database. Remember that the datbase is in two files. If the database is called abc, then you'll have two files: abc.0 and abc.0.aux. (the zero can be a different number)
Note that you can specify a search path to find traces, but by default it looks for them in the same directory as the gap4 assembly database (the dbname.0 and dbname.0.aux files).
The main gain options menu (probably only once in expert mode via "configure menu") has an option to adjust the search path. Alternatively you can set the RAWDATA environment variable.
If you want an example of how this works look at the demo/gap4 directory and you'll see that the traces have been archived up in a unix tar file, but gap4 still displays them.
There's some info here on this:
Also note that you can specify some other access methods (poorly documented it seems).
Tar files: You can add a search path of "TAR=filename.tar" and it'll look for the trace filename inside a unix tar named "filename.tar". If there's a filename.tar.index (created by index_tar) then the lookup will be quicker.
URLs: "URL=http://blah/whatever.cgi?trace=%s" for example will replace the %s with the trace name with the trace name and use the unix wget utility to fetch the trace remotely. This is convenient as it effectively allows you to write a web interface to any external trace repository and get gap4 fetching traces out on-the-fly. It isn't ideal though due to the dependancy on wget.
File hashes (latest io_lib only): "HASH=archive.hash". This is similar to index_tar and TAR=, except the hash is an index to an arbitrary archive of whatever format (provided the entire file isn't compressed). Utility programs hash_tar and hash_tvf (for 454 TVF archives) exist to create the .hash file. Performance of extracting traces out of a tar file like this is extremely good and it scales up well. Tested against EXT3 it works out substantially faster than raw filesystem access.
There's also ARC=machine/port for access to the ENSEMBL trace archive via the pfetch interface (possibly this only works locally - untested).
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