As originators of this thread here is what we have found thus far.
We found a really useful example in Staden/testpackage/gap that got things
rolling. From it I was able to start a project, and produce this outline.
Project outline:
1. create a project directory
2. copy ABI files into directory (can also use SCF files)
3. make a project file which lists each ABI or SCF file (all of one type)(exp. t.shotgun)
4. copy sequencing vector and cosmid vector sequance files into directory
(format ;coment line, followed by sequance) (exp. m13mp18.vec lorist6.vep
5. run pregap,
PreGap V1.3
File of filenames to be used: t.shotgun
Trace file type (ABI, ALF, EXP, PLN, or SCF) [ABI]: SCF
Quality clipping required? [Yes]:
Locate and mark sequencing vector [Yes]:
Sequence vector file: m13mp18.vec
Sequence vector cloning site: 6249
Sequence vector primer site: 41
Locate and mark cloning vector [Yes]:
Cloning vector file: lorist6.vep
Screen against vector [No]: Yes
ALU tagging required? [No]:
output files are t.shotgun.passed t.shotgun.failed t.shotgun.scf and t.shotgun.exp
6. run xgap
open a new database for DNA
go Modification->Auto assemble
Permit entry = yes
Show all alignments
Use file of file names? = Yes
File of gel reading names? t.shotgun.passed
File for names of failures t.shotgun.failed2
Preform normal shotgun assembly
Permit joins = yes
Reject failures
Minimum initial match= 15
Maximum pads per gel= 8
Maximum pads per gel in contig= 8
Maximum percent mismatch after alignment =8.00
7. now explore, edit contig, join contig, etc.
FOR THE STADEN EXPERTS, this question: How do we now list contigs?
Thanks,
Robert Hooper
Ned Lally
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Robert Hooper | "The Hitchhiker's Guide to the Galaxy"-
University of Pennsylvania |
4010 Locust Street | "We'll be saying a big hello to all
Philadelphia, PA 19104 | intelligent life forms everywhere..."
phone: (215) 898-4402 | "and to everyone else out there,
fax: (215) 898-3695 | the secret is to bang the rocks together,
robert at biochem.dental.upenn.edu | guys."
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