Problems w/phrap reassembly in Gap4

James Bonfield jkb at mrc-lmb.cam.ac.uk
Thu Jan 27 05:14:00 EST 2000

In article <86hqfd$3i4$1 at mercury.hgmp.mrc.ac.uk> Paul Shinn <pshinn at mail1.sas.upenn.edu> writes:
>    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?

I believe Matthew Betts is already helping you on this issue, but for
the benefit of other readers of this forum I'll explain a bit more

The documentation explains the list of tasks which the Phrap
Reassembly task performs. This task list (extract readings,
disassembly, phrap, directed assembly) is automatically performed by
one single use of Phrap Reassembly, so you should not need to deal
with the individual steps yourself. (They are outlined in the manual
purely as a means of documenting what is going on behind the scenes.)

James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/

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