extract_seq - is it broken?

Andy Law Andy.Law at bbsrc.ac.uk
Fri Feb 7 04:23:48 EST 1997

In article <5dcod8$ldh at lyra.csx.cam.ac.uk>, jkb at mrc-lmb.cam.ac.uk (James
Bonfield) wrote:

 >  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.

If I do split my sequence files in this way, will gap assemble them correctly?

Andy Law
( Andy.Law at bbsrc.ac.uk )
( Big Nose in Edinburgh )

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