PileUp's maximum sequence length is 5kb. I don't know if it can be
changed. It's a lousy parameter, as I have 10-20kb I'd like to see too.
Please let me know if you find a better way. I'll be watching the net --
does anyone know a better way?
jknott at molbio.cbs.umn.edu
On 16 Nov 1994 jcalvert at crcvms.unl.edu wrote:
> What's the most likely cause of the "alignment may not
> be optimal" message during a pileup alignment of several
> long sequences? The resulting output is clearly not the
> best alignment. Is this a memory problem? What parameter
> needs to be increased?
>> Thanks in advance for helpful suggestions from anyone.
>> Jay Calvert jcalvert at crcvms.unl.edu>>>