SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
how to use bambus for scaffolding? elisadouzi Bioinformatics 3 05-31-2013 03:07 PM
MUMmer VS blastp anyone1985 Bioinformatics 13 02-11-2013 08:52 AM
Viewing Mummer Aligments twaddlac Bioinformatics 0 02-03-2012 06:27 AM
Global Alignment With Mummer (Parameter for Gap Extension & Opening Cost) peveralldubois Bioinformatics 0 03-07-2011 12:45 AM
euler-sr scaffolding tshea Bioinformatics 2 06-11-2009 11:27 AM

Reply
 
Thread Tools
Old 04-13-2012, 04:46 AM   #1
rahularjun86
Member
 
Location: Frankfurt(M), Germany

Join Date: Jan 2011
Posts: 58
Default 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
__________________
Rahul Sharma,
Ph.D
Frankfurt am Main, Germany
rahularjun86 is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:20 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO