splitseq_da

James Bonfield jkb at arran.mrc-lmb.cam.ac.uk
Wed May 10 03:31:49 EST 2000


In <3917FDB3.3F08A1B4 at uni-essen.de> guido.marquitan at uni-essen.de (gmq) writes:

> and gap4 to handle, so I would like to split them into smaller
> overlapping portions with splitseq_da.
> Unfortunately, there is no kind of description for this handy script.
> How can I use it, and what arguments does it need?

Apologies - we have no documentation for it yet. However typing "splitseq_da"
by itself and looking at the source for the script "more `which splitseq_da`"
should help.

In short, just run "splitseq_da filename" where filename is the name of a file 
containing a single plain-text sequence or one or more fasta sequences. It
will then produce a series of experiment files based with filenames derived
from the input data and a filename.fofn file ("filename" being whatever was
specified as the argument to splitseq_da). It is recommended that you enter
this data into Gap4 using directed assembly (although normal shotgun assembly
will also work, albeit with an unnecessary amount of computation).

     James
--
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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