I am looking at synteny inside Aristolochia genome and the gene order is not conserved in the area I am looking at. So I tried using the synteny mode instead of the collinearity one.
However, since I get many detections with default parameters I tried being more restrictive by enhancing the number of anchor points (among other things). It seems that no matter the number of anchor points I set I still get clouds with at least 3 anchor points. I don't experience this behaviour with the collinearity mode.
Is this behaviour expected ?
the parameters I used:
i-ADHoRe parameters
Number of genelists = 7
Blast table = families_blast_orthofinder.tsv
Output path = unassigned/plaza/aristolochia_61460_synteny_25_6_1e-3_q085/
Gap size = 0
Cluster gap size = 0
Cloud gap size = 25
Cloud cluster gap size = 30
Max gaps in alignment = 0
Tandem gap = 15
Flush output = 1000
Q-value = 0.85
Anchorpoints = 6
Probability cutoff = 0.001
Cloud filtering method = Binomial
Level 2 only = true
Use family = true
Write statistics = true
Alignment method = GreedyGraphbased4
Multiple hypothesis correction = FDR
Number of threads = 4
Compare aligners = false
Synthenic cloud searches only
Visualize GHM.png = false
Visualize Alignment = true
Verbose output = true
**** END i-AdDHoRe parameters *****
Dear authors,
I am using the docker version of i-adhore 3.0
I am looking at synteny inside Aristolochia genome and the gene order is not conserved in the area I am looking at. So I tried using the synteny mode instead of the collinearity one.
However, since I get many detections with default parameters I tried being more restrictive by enhancing the number of anchor points (among other things). It seems that no matter the number of anchor points I set I still get clouds with at least 3 anchor points. I don't experience this behaviour with the collinearity mode.
Is this behaviour expected ?
the parameters I used: i-ADHoRe parameters Number of genelists = 7 Blast table = families_blast_orthofinder.tsv Output path = unassigned/plaza/aristolochia_61460_synteny_25_6_1e-3_q085/ Gap size = 0 Cluster gap size = 0 Cloud gap size = 25 Cloud cluster gap size = 30 Max gaps in alignment = 0 Tandem gap = 15 Flush output = 1000 Q-value = 0.85 Anchorpoints = 6 Probability cutoff = 0.001 Cloud filtering method = Binomial Level 2 only = true Use family = true Write statistics = true Alignment method = GreedyGraphbased4 Multiple hypothesis correction = FDR Number of threads = 4 Compare aligners = false Synthenic cloud searches only Visualize GHM.png = false Visualize Alignment = true Verbose output = true **** END i-AdDHoRe parameters *****
and I get results in the clouds.txt file like this (this is just the beginning of the file): id genome_x list_x genome_y list_y number_of_anchorpoints cloud_density dim_x dim_y 1 afi 2 afi 2 53 0.317365 328 167 2 afi 2 afi 2 41 0.577465 71 206 3 afi 2 afi 2 37 0.72549 193 51 4 afi 2 afi 2 16 0.225352 95 71 5 afi 2 afi 2 24 0.230769 176 104 6 afi 2 afi 2 15 0.214286 88 70 7 afi 2 afi 2 14 0.285714 125 49 8 afi 2 afi 2 64 0.412903 155 264 9 afi 2 afi 2 3 1 3 3 10 afi 2 afi 2 17 0.223684 171 76 11 afi 2 afi 2 5 0.277778 18 18 12 afi 2 afi 2 9 0.214286 73 42 13 afi 2 afi 2 7 0.225806 47 31 14 afi 2 afi 2 5 0.25 20 21 15 afi 2 afi 2 5 0.238095 21 21 16 afi 2 afi 2 4 0.4 10 20 17 afi 2 afi 2 4 0.571429 7 29 18 afi 2 afi 2 3 1.5 24 2 19 afi 2 afi 2 9 0.2 45 84
Maybe there is an option I missed... Thank you for your help !
Marie