Mauve stuff: Difference between revisions
From MDWiki
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
Feature Matrix in Genoplast format | |||
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 | 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.locs has the genomic coordinates of the features | ||
27_my_feats.bin is the binary presence/absence matrix | 27_my_feats.bin is the binary presence/absence matrix | ||
Extract an XFMA containing only the core genome regions | Extract an XFMA containing only the core genome regions | ||
| Line 10: | Line 14: | ||
./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 | ./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 | ||
2) Reconstruct the backbone file with progressiveMauve | |||
./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 | ||
3) Run stripSubsetLCBs to strip out regions present in < 27 organisms | |||
./stripSubsetLCBs new_27_somebugs_with_bb new_27_somebugs_with_bb.bbcols my_27_core.xmfa | ./stripSubsetLCBs new_27_somebugs_with_bb new_27_somebugs_with_bb.bbcols my_27_core.xmfa | ||
Latest revision as of 01:09, 2 July 2009
Feature Matrix in Genoplast format
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
2) Reconstruct the backbone file with progressiveMauve
./progressiveMauve --apply-backbone=new_27_somebugs_bb --output=new_27_somebugs_with_bb
3) Run stripSubsetLCBs to strip out regions present in < 27 organisms
./stripSubsetLCBs new_27_somebugs_with_bb new_27_somebugs_with_bb.bbcols my_27_core.xmfa
