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-   -   Mummer promer for scaffolding (http://seqanswers.com/forums/showthread.php?t=19197)

rahularjun86 04-13-2012 04:46 AM

Mummer promer for scaffolding
 
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:
HTML Code:

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:
HTML Code:

>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:

HTML Code:

  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


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