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:
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:
Parsed Alignment file:
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
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
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
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
I will really appreciate your help regarding this.
Thanks,
Rahul