Mummer promer for scaffolding

[rahularjun86]

Dear members,
I am using Mummer promer program to do scaffolding of a genome from two closely related references. I generated the tiling file from show-tiling. Then I wrote a perl script for ordering and orientation of query contigs according to reference. But I am getting many values as -ve in the 3rd column of the tiling file and when I crosschecked this from alignment file, the alignment region was not overlapping and co-ordinates were not matching in both files.

I used the following commands:

promer -p test_promer_mumref ../t1_contigs.fa ../t2_contigs.fasta
show-tiling test_promer_mumref.delta > test_promer_mumref.tiling
show-tiling -a test_promer_mumref.delta > test_promer_mumref.tiling

How does MUMmer promer generate tiling file's 3rd column, Does it consider the size of the contigs? Why the co-ordinates are not matching with the alignment file's co-ordinates after adding lengths of the contigs?


Here is my tiling file for 1st Chromosome:

>chr01 2476500 bases
-12758  677741  -12603  690500  44.15   67.67   -       scaffold1|size690500
665139  869316  -2005   204178  53.10   65.50   -       scaffold16|size204178
867312  881226  325     13915   42.21   70.64   -       scaffold208|size13915
881552  948717  -7662   67166   68.58   69.28   -       scaffold105|size67166
941056  1087208 4890    146153  51.10   66.69   +       scaffold36|size146153
1092099 1152234 -1981   60136   61.21   64.07   +       scaffold112|size60136
1150254 1259031 8157    108778  55.73   66.37   -       scaffold54|size108778
1267189 1282216 -7275   15028   45.48   62.88   -       scaffold204|size15028
1274942 1320522 346     45581   63.66   68.00   +       scaffold139|size45581
1320869 1328148 1716    7280    65.38   67.01   -       scaffold236|size7280
1329865 1358660 -1836   28796   48.84   65.00   -       scaffold178|size28796
1356825 1371653 -3075   14829   78.11   63.32   +       scaffold205|size14829
1368579 1468814 9674    100236  32.33   62.98   -       scaffold62|size100236
1478489 1529554 7784    51066   50.13   68.99   -       scaffold128|size51066
1537339 1704000 -6413   166662  34.98   68.35   -       scaffold26|size166662
1697588 1779202 -311    81615   41.74   67.04   +       scaffold81|size81615
1778892 1904947 -4899   126056  51.10   67.28   -       scaffold44|size126056
1900049 1915711 -5874   15663   46.58   64.63   -       scaffold202|size15663
1909838 1971171 -2046   61334   37.92   70.21   -       scaffold109|size61334
1969126 2004295 -6537   35170   56.66   65.55   -       scaffold164|size35170
1997759 2209497 3599    211739  56.48   67.86   -       scaffold39|size211739
2213097 2391413 -1650   178317  55.40   67.29   +       scaffold22|size178317
2389764 2461175 15325   71412   55.22   71.74   +       scaffold88|size71412

Parsed Alignment file:

   1 62264   63145   675928  675041  882     888     82.27   2476500 690500  0.04    0.13    chr01   scaffold1|size690500
   2 662239  664896  3185    528     2658    2658    70.77   2476500 690500  0.11    0.38    chr01   scaffold1|size690500
   3 
   4 665520-664896=624
   5 
   6 665520  666275  204167  203349  756     819     65.33   2476500 204178  0.03    0.40    chr01   scaffold16|size204178
   7 860958  864164  4190    960     3207    3231    73.94   2476500 204178  0.13    1.58    chr01   scaffold16|size204178
   8 
   9 869984-864164=5820
  10 
  11 869984  870169  10047   9871    186     177     58.06   2476500 13915   0.01    1.27    chr01   scaffold208|size13915
  12 879063  880988  2164    161     1926    2004    70.39   2476500 13915   0.08    14.40   chr01   scaffold208|size13915
  13 
  14 881378-880988=390
  15 
  16 881378  883582  67025   64797   2205    2229    88.05   2476500 67166   0.09    3.32    chr01   scaffold105|size67166
  17 942271  945909  3636    31      3639    3606    56.28   2476500 67166   0.15    5.37    chr01   scaffold105|size67166
  18 
  19 946696-945909=787
  20 
  21 946696  948459  276     2054    1764    1779    73.28   2476500 146153  0.07    1.22    chr01   scaffold36|size146153
  22 1090189 1090410 144255  144473  222     219     52.70   2476500 146153  0.01    0.15    chr01   scaffold36|size146153
  23 
  24 1092931-1090410=2521
  25 
  26 1092931 1094592 1287    2969    1662    1683    56.22   2476500 60136   0.07    2.80    chr01   scaffold112|size60136
  27 1146896 1150690 54573   58235   3795    3663    52.20   2476500 60136   0.15    6.09    chr01   scaffold112|size60136
  28 

If we compare the co-ordinates by adding contig size to the alignment co-ordinates they are not same to tiling file?

I will really appreciate your help regarding this.

Thanks,
Rahul