We are using the Staden package to assemble a 950 kb bacterial genome. We have primer-walked across a number of 8-kb insert clones to resolve misassemblies and close gaps. Is it possible to assemble the primer-walked clones as fasta files together with the .exp files from the shotgun reads? When we tried doing this using Phrap launched from gap4, we got the following error message:
Error in Tcl Script
Error: child process excited abnormally
Thanks for your help,
The "child process" here will be Phrap,but I'm not sure why it is failing. There may still be the input files left in the current directory (or an appropriately named subdirectory - I forget) which will aid debugging.
Regardless of this, the way to mix experiment files and fasta files together is to use Pregap4 first as this automatically converts fasta into (possibly several) experiment files. Pregap4 also has a direct interface to running Phrap if you wish.