Dpuiu alignment

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Revision as of 16:04, 30 September 2009 by Dpuiu (talk | contribs)
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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)
 W:        max window size (default 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