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Pileup Help!

Michael J. Weise weise at BSCR.UGA.EDU
Mon Apr 24 07:56:19 EST 1995


>   Essentially I have a file containing 192 sequence names. I have
>manually taken out those sequences that are greater than 7000 bp., and
>attempted to do a pileup with the command:
>
>pileup @ptp.str4 -MAXS=7000
>
>However the program comes back with the message: Error greater than 0 gap
>insertions.
>
>   I apologize if this is an obvious question that has previously been 
>answered.
>
>   Thanks.
>
>Mukul Ranjan
>ranjan at helix.nih.gov

	In the on-line help for Pileup under Restrictions, there's a discussing 
of the MAXSegs and MAXGaps parameters.  It looks to me as though setting MAXSegs 
to 7000 automatically reduces the allowable number of gaps per sequence to zero. 
The sequence set defined in ptp.str4 must need some gaps, but since Pileup's run 
without allowing any the program dies.

		MJW
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 / Michael J. Weise, Ph.D.    \   Biological Sciences Computing Recource   \
(   weise at bscr.uga.edu         \   Dept.of Genetics  UGa, Athens  GA  30602 )
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