Dpuiu alignment: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 2: | Line 2: | ||
Programs: | Programs: | ||
* filter-anc.pl -max | * filter-anc.pl -max -percent -w -W | ||
max: max distance between the ref_intercept (default 1,000,000) | max: max distance between the ref_intercept (default 1,000,000) | ||
percent: min pc of disagreements for deleting an alignment (default 25) | percent: min pc of disagreements for deleting an alignment (default 25) | ||
| Line 8: | Line 8: | ||
W: max window size (default 100) | W: max window size (default 100) | ||
* merge-anc.pl -max | * merge-anc.pl -max | ||
max: max distance between the ref_intercept (default 1,000,000) | max: max distance between the ref_intercept (default 1,000,000) | ||
Revision as of 16:01, 30 September 2009
Filtering
Programs:
- filter-anc.pl -max -percent -w -W
max: max distance between the ref_intercept (default 1,000,000) percent: min pc of disagreements for deleting 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