Problems w/phrap reassembly in Gap4

Paul Shinn pshinn at mail1.sas.upenn.edu
Mon Jan 24 09:47:24 EST 2000

    We're using an in-house perl script that uses the old-format ace 
file from phrap to output an ordered list of Gap4 experimental files.  
That list is then read into a new Gap4 database using the Directed 
Assembly function.
    After we've done a number of finishing reactions, we manually
incorporate each read into the Gap4 database using the Join Editor.  As
you can imagine this is very tedious.  Well, I wish to use the Phrap
Reassembly option in Gap4 to automate this .....chore.  I could rephrap
and then reimport in the new assembly but then I lose ALL the tags I had
in Gap4.  It's as tedious to put them back in.  So I downloaded the
gcphrap modules from Staden and I've recompiled phrap to get the gcphrap
binary.  That was easy.  What's not so easy is to figure out the
instructions in the Gap4 manual. 
    Since these finishing reactions span the whole assembly and are not
concentrated in one locale, I make a list of ALL the reads in the
database (List-->Contigs to Readings).  Following that step you Extract
Readings to a folder.  This writes all your readings to experimental
files to a specified folder preserving your tags.  Then you disassemble
these readings from your database and end up with an empty database. 
Finally, you're supposed to do the Phrap Reassembly.  You tell the 
dialox the name of the file containing the reading names to be reassembled 
and then a destination directory where it should rewrite the 
experimental files.  OK, easy enough.  However, the error window says it 
can not find any of the files listed.  I know they are there.
    Can anyone help me out on this?


Paul Shinn    
Sequencing Coordinator                                    ,___o
pshinn at neomorph.bio.upenn.edu                            _-\_<,
Arabidopsis thaliana Genome Center                      (*)/'(*)
(215) 573-7256

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