Mauve stuff: Difference between revisions
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./progressiveMauve --apply-backbone=new_27_somebugs_bb --output=new_27_somebugs_with_bb | ./progressiveMauve --apply-backbone=new_27_somebugs_bb --output=new_27_somebugs_with_bb | ||
./ | ./stripSubsetLCBs new_27_somebugs_with_bb new_27_somebugs_with_bb.bbcols my_27_core.xmfa | ||
Revision as of 00:32, 2 July 2009
bbFilter somebugs_bb.backbone 50 27_my_feats.bin gp 1 2 3 4 5 6 7 8 10 11 12 13 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29
27_my_feats.bin.locs has the genomic coordinates of the features
27_my_feats.bin is the binary presence/absence matrix,
Extract an XFMA containing only the core genome regions
1) Use projectandStrip to project the 31-way alignment down to a 27-way
./projectAndStrip somebugs_bb new_27_somebugs_bb 1 2 3 4 5 6 7 8 10 11 12 13 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29
./progressiveMauve --apply-backbone=new_27_somebugs_bb --output=new_27_somebugs_with_bb
./stripSubsetLCBs new_27_somebugs_with_bb new_27_somebugs_with_bb.bbcols my_27_core.xmfa
