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Help w/ a first time sequencing project, part deux

Ned Lally lally at toxin.dental.upenn.edu
Wed Mar 15 16:19:57 EST 1995

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?

Robert Hooper
Ned Lally 
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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