Manage dotplot windowsize about yass HOT 1 CLOSED

Hi,

there is not windowsize as in a "true" dotplot, since it is an alignment tool provided with a dotplot viewer

you can change virtually the windowsize :

• directly in the dotplot tool (online or remote) to filter out yass results :
  • by using the &maxAl=10000 parameter (add it directly in the URL), to show only 10000 most relevant alignments
  • by adding the maxAl=10000 parameter, to the https://github.com/laurentnoe/yass/blob/master/yass2dotplot.php command line tool

• possibly in yass to get better parameters for what you expect to align :
  • by modifying the E-value (e.g. -E 1e-6 or -E 1e-9)
  • by changing the scoring system to something more or less stringent ( e.g -C 1,-3 -G 8,2 or -C 1,-1 -G 2,1)
  • possibly by changing the indels and mutation parameters (e.g -i 10 -m 5 ), and possibly by disabling the post-processing step (e.g. -w 0)

PS : where is the " is:issue wdsize.mat" file ?

from yass.