extract_seq - is it broken?

James Bonfield jkb at mrc-lmb.cam.ac.uk
Thu Feb 6 09:04:24 EST 1997

In article <Andy.Law-ya023480000602971241190001 at is.bbsrc.ac.uk> Andy.Law at bbsrc.ac.uk (Andy Law) writes:
>I can't seem to get extract_seq to take notice of the CS tags when
>specifying the -good_only option. It just ignores them completely. Gap4
>seems to ignore them too on occasion.

You need to also use the -clip_cosmid option. This wasn't in earlier
versions of extract_seq. The reasoning is that it's sometimes useful
to keep the cosmid sequence. This is even true in gap4 where leaving
the cosmid sequence in allows you to easily see the cosmid ends and
hence find the correct placement of at least two contigs.

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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