Dpuiu alignment

Filtering

Programs:

• filter-anc.pl -max -percent -w -W

 max:      max distance between the ref_intercept (default 1,000,000)
 percent:  min percent agreement for keeping an alignment (default 25)
 w:        min window size (default 4)   => 1+w*2
 W:        max window size (default 100) => 1+W*2

 Bacterial genomes (few Mbp) use -max 100000  -W 10
 Mammalian genomes (few Gbp) use -max 1000000 -W 100 
 

• merge-anc.pl -max

 max:      max distance between the ref_intercept (default 1,000,000)

• Example:

 cat PA14-PA7.delta     | ~/bin/shrinkIds.pl | ~/bin/DELTA/delta2anc.pl > PA14-PA7.anc 
 cat PA14-PA7.anc       | ~/bin/DELTA/filter-anc.pl -max 100000 -W 10   > PA14-PA7.filter.anc
 PA14-PA7.filter.anc    | ~/bin/DELTA/merge-anc.pl -max 100000          > PA14-PA7.merge.anc
 cat PA14-PA7.merge.anc | ~/bin/DELTA/anc2delta.pl                      > PA14-PA7.merge.delta

 wc -l *anc
  691 PA14-PA7.anc
  528 PA14-PA7.filter.anc
    9 PA14-PA7.merge.anc