Skip to content
Snippets Groups Projects

Compare revisions

Changes are shown as if the source revision was being merged into the target revision. Learn more about comparing revisions.

Source

Select target project
No results found

Target

Select target project
  • cpv616/module1_2
  • nma904/module1_2
2 results
Show changes
Showing
with 468 additions and 167 deletions
chr size
1 19561049
2 20977047
3 37318896
4 34047100
5 21375137
6 28584509
7 26440503
8 28358298
9 26458845
10 21706344
11 21697428
12 21470783
13 18106809
14 20802709
\ No newline at end of file
quisa.S10.gnm1.Chr01 19561049
quisa.S10.gnm1.Chr02 20977047
quisa.S10.gnm1.Chr03 37318896
quisa.S10.gnm1.Chr04 34047100
quisa.S10.gnm1.Chr05 21375137
quisa.S10.gnm1.Chr06 28584509
quisa.S10.gnm1.Chr07 26440503
quisa.S10.gnm1.Chr08 28358298
quisa.S10.gnm1.Chr09 26458845
quisa.S10.gnm1.Chr10 21706344
quisa.S10.gnm1.Chr11 21697428
quisa.S10.gnm1.Chr12 21470783
quisa.S10.gnm1.Chr13 18106809
quisa.S10.gnm1.Chr14 20802709
\ No newline at end of file
chr size
1 57468748
2 51272464
3 49996358
4 48286772
5 45669363
6 45655421
7 41929180
\ No newline at end of file
cerca.ISC453364.gnm3.Chr01 57468748
cerca.ISC453364.gnm3.Chr02 51272464
cerca.ISC453364.gnm3.Chr03 49996358
cerca.ISC453364.gnm3.Chr04 48286772
cerca.ISC453364.gnm3.Chr05 45669363
cerca.ISC453364.gnm3.Chr06 45655421
cerca.ISC453364.gnm3.Chr07 41929180
\ No newline at end of file
chr size
1 136071090
2 116487353
3 109186524
4 91914064
5 88658134
6 84872623
7 83373435
8 81990953
9 76993406
10 75912673
11 75144154
12 71117942
\ No newline at end of file
singl.CAF01.gnm1.Chr01 136071090
singl.CAF01.gnm1.Chr02 116487353
singl.CAF01.gnm1.Chr03 109186524
singl.CAF01.gnm1.Chr04 91914064
singl.CAF01.gnm1.Chr05 88658134
singl.CAF01.gnm1.Chr06 84872623
singl.CAF01.gnm1.Chr07 83373435
singl.CAF01.gnm1.Chr08 81990953
singl.CAF01.gnm1.Chr09 76993406
singl.CAF01.gnm1.Chr10 75912673
singl.CAF01.gnm1.Chr11 75144154
singl.CAF01.gnm1.Chr12 71117942
\ No newline at end of file
chr size
1 32816166
2 42009719
3 37860065
4 30689712
5 52777034
6 46512068
7 30975534
8 49705205
9 35860388
10 41499577
11 30871617
12 29799933
13 41270226
\ No newline at end of file
sento.Myeongyun.gnm1.Chr01 32816166
sento.Myeongyun.gnm1.Chr02 42009719
sento.Myeongyun.gnm1.Chr03 37860065
sento.Myeongyun.gnm1.Chr04 30689712
sento.Myeongyun.gnm1.Chr05 52777034
sento.Myeongyun.gnm1.Chr06 46512068
sento.Myeongyun.gnm1.Chr07 30975534
sento.Myeongyun.gnm1.Chr08 49705205
sento.Myeongyun.gnm1.Chr09 35860388
sento.Myeongyun.gnm1.Chr10 41499577
sento.Myeongyun.gnm1.Chr11 30871617
sento.Myeongyun.gnm1.Chr12 29799933
sento.Myeongyun.gnm1.Chr13 41270226
\ No newline at end of file
chr size
1 47851208
2 30405870
3 27368013
4 25843236
5 18496696
6 30767194
7 22388614
8 22573980
\ No newline at end of file
prupe.Lovell.gnm2.Pp01 47851208
prupe.Lovell.gnm2.Pp02 30405870
prupe.Lovell.gnm2.Pp03 27368013
prupe.Lovell.gnm2.Pp04 25843236
prupe.Lovell.gnm2.Pp05 18496696
prupe.Lovell.gnm2.Pp06 30767194
prupe.Lovell.gnm2.Pp07 22388614
prupe.Lovell.gnm2.Pp08 22573980
\ No newline at end of file
chr size
1 51433939
2 49670989
3 53438756
4 48048378
5 40923498
6 31236378
7 40041001
8 63048260
9 38250102
10 44302882
11 53580169
\ No newline at end of file
phavu.G19833.gnm2.Chr01 51433939
phavu.G19833.gnm2.Chr02 49670989
phavu.G19833.gnm2.Chr03 53438756
phavu.G19833.gnm2.Chr04 48048378
phavu.G19833.gnm2.Chr05 40923498
phavu.G19833.gnm2.Chr06 31236378
phavu.G19833.gnm2.Chr07 40041001
phavu.G19833.gnm2.Chr08 63048260
phavu.G19833.gnm2.Chr09 38250102
phavu.G19833.gnm2.Chr10 44302882
phavu.G19833.gnm2.Chr11 53580169
\ No newline at end of file
chr size
1 52991155
2 45729672
3 55515152
4 56582383
5 43630510
6 35275713
7 49172423
8 45569985
\ No newline at end of file
medtr.A17_HM341.gnm4.chr1 52991155
medtr.A17_HM341.gnm4.chr2 45729672
medtr.A17_HM341.gnm4.chr3 55515152
medtr.A17_HM341.gnm4.chr4 56582383
medtr.A17_HM341.gnm4.chr5 43630510
medtr.A17_HM341.gnm4.chr6 35275713
medtr.A17_HM341.gnm4.chr7 49172423
medtr.A17_HM341.gnm4.chr8 45569985
\ No newline at end of file
chr size
1 23037639
2 18779844
3 19341862
4 23867706
5 25021643
6 21508407
7 21026613
8 22385789
9 23006712
10 18140952
11 19818926
12 22702307
13 24396255
14 30274277
15 20304914
16 22053297
17 17126926
18 29360087
19 24021853
\ No newline at end of file
vitvi.PN40024.gnm2.chr1 23037639
vitvi.PN40024.gnm2.chr2 18779844
vitvi.PN40024.gnm2.chr3 19341862
vitvi.PN40024.gnm2.chr4 23867706
vitvi.PN40024.gnm2.chr5 25021643
vitvi.PN40024.gnm2.chr6 21508407
vitvi.PN40024.gnm2.chr7 21026613
vitvi.PN40024.gnm2.chr8 22385789
vitvi.PN40024.gnm2.chr9 23006712
vitvi.PN40024.gnm2.chr10 18140952
vitvi.PN40024.gnm2.chr11 19818926
vitvi.PN40024.gnm2.chr12 22702307
vitvi.PN40024.gnm2.chr13 24396255
vitvi.PN40024.gnm2.chr14 30274277
vitvi.PN40024.gnm2.chr15 20304914
vitvi.PN40024.gnm2.chr16 22053297
vitvi.PN40024.gnm2.chr17 17126926
vitvi.PN40024.gnm2.chr18 29360087
vitvi.PN40024.gnm2.chr19 24021853
\ No newline at end of file
# project name
project_name: "project-monocots"
project_name: "project-buxus"
# input : path to genome information file
input_file:
......@@ -52,21 +52,21 @@ gf3: 1
K: 7
## set thresholds
ctgLen: 1 ## minimum length in each contig
nctg: 250 ## only include first nctg contigs
#ctgLen: 1 ## minimum length in each contig
#nctg: 250 ## only include first nctg contigs
## threshold of distance (1MB) between two genes in the same contig on the same chromosome
## if the distance between two genes is smaller than the threshold, merge them into one block
DIS.threshold: 1000000
#DIS.threshold: 1000000
## threshold to visualize the gene/block (150 kb)
## if a block is less than this length, do not show it --> keep the plot clean
blockLEN.threshold: 150000
#blockLEN.threshold: 150000
## threshold for coocurrence analysis
## only count blocks that are longer than 15KB
lenBLK.threshold: 15000
#lenBLK.threshold: 15000
......
chr size
LG01 24880688
LG02 17334668
LG03 16781886
LG04 15584765
LG05 15024279
LG06 14747297
LG07 14728688
LG08 13970067
LG09 13841557
LG10 13112115
LG11 13096665
LG12 12612916
LG13 11759267
LG14 11705491
LG15 11365478
LG16 11174208
LG17 11156084
LG18 10911977
LG19 10815949
LG20 10792357
LG21 10645290
LG22 10398566
LG23 7979763
LG24 7684463
LG25 3739203
chr size
REF_ELAGV01 68435666
REF_ELAGV02 65558141
REF_ELAGV03 60060032
REF_ELAGV04 57251647
REF_ELAGV05 51955539
REF_ELAGV06 44357769
REF_ELAGV07 43454766
REF_ELAGV08 40195399
REF_ELAGV09 38056896
REF_ELAGV10 31890735
REF_ELAGV11 30068910
REF_ELAGV12 28800575
REF_ELAGV13 27817470
REF_ELAGV14 24379743
REF_ELAGV15 24314465
REF_ELAGV16 21371083
chr size
AsparagusV1_01 132393784
AsparagusV1_02 84732013
AsparagusV1_03 113259003
AsparagusV1_04 146560859
AsparagusV1_05 131469567
AsparagusV1_06 78779235
AsparagusV1_07 151357931
AsparagusV1_08 131339754
AsparagusV1_09 68543460
AsparagusV1_10 73452336
chr size
1 31431123
2 33969142
3 19547260
4 27749968
5 32871075
6 32866201
7 18053115
8 28021425
9 23324680
10 17904088
11 17195437
12 25272979
13 29719729
14 15713101
15 10474557
16 23371965
17 20585887
18 22795539
19 9927364
20 10677198
21 5203141
chr size
1 11560055
2 8180930
3 8870115
4 9537711
5 7072156
6 8333076
7 7949387
8 8482602
9 7754086
10 7963964
11 6749155
12 5993893
13 6317482
14 5575328
15 4557367
16 5820572
17 4601490
18 5315945
19 3959434
20 3997407
chr size 1 37743429 2 34360390 3 33772675 4 31994915 5 31167455 6 30970160 7 30771956 8 28400560 9 28235908 10 25518903 11 25169648 12 24790462
\ No newline at end of file
......@@ -81,7 +81,7 @@ class Genome:
f.write(chromosome + " ")
for gene in genes:
f.write("%s " % genes)
f.write("%s " % gene)
f.write("\n")
......
This diff is collapsed.