question about varied results

[jenny315]

Hello, Professor，

I have some questions about the result. Could you please give some stuggestion for me

• My results are summarised below， when Block resolution is 50k, the result I got (form file APCF_size.txt) 609 APCFs total 228079891 bp. when Block resolution is 100K, the result I got (form file APCF_size.txt) 135 APCFs total 140661249 bp. when Block resolution is 300k, the result I got (form file APCF_size.txt) 56 APCFs total 64342708 bp.

• My questions are summarised below,

  1. I'm getting varied results with different resolutions, the amount and total length of APCFs are quite inconsistent. Is this normal? Maybe these results aren't usable at all.
  2. I know there can't be so many ancestral chromosomes (even up to 600). Therefore, I'm not sure which results to use.
  3. Even the biggest result obtained here (609 APCFs, comprising 228079891 bp) is still quite small (in comparison to the genome size of the species used). Is this normal? Or would you suggest me to adjust the parameters further?

• The genome size and chromosome number of the selected species are as follows, respectively：

  name    sum_leh chr_num
  Ly  668,967,811 24
  Cs  445,139,357 22
  Dr  1,345,101,833   25
  Gg  1,100,911,310   40
  Lo  891,144,077 29
  Lp  625,267,304 24
  Ol  734,040,372 24
  Tr  281,572,362 22

• Species relationships and ancestor node settings@ marker are detailed in the files "config.SFs" and "tree.txt"

• • config.SFs

    
    # path of a net files
    >netdir
    /data/jenny/61MD5jenny/deschr/02spec/chainNet

path of a chain files

chaindir /data/jenny/61MD5jenny/deschr/02spec/chainNet

species-name tag1 tag2

tag1 (0: ref-species, 1: descendents, 2: outgroup)

tag2 (1: chromosome assembly, 0: others)

Warning for tag2: Use the value 1 only when a chromosome name starts with "chr".

species Ly 0 1 Cs 1 1 Dr 1 1 Gg 2 1 Lo 1 1 Lp 1 1 Ol 1 1 Tr 1 1

bLok resolution (bp): DO NOT CHANGE

resolution

``` - - tree.txt ``` (((((((Ly:0.00582,Lp:0.01924):0.05216,Tr:0.12628):0.01846,Cs:0.13082):0.01913,Ol:0.12087):0.10993,Dr:0.1699):0.08193,Lo:0.13718)@:0.103875,Gg:0.120100); ``` Many thanks, I appreciate your prompt response. Jenny

[jkimlab]

The total length depends on the total length of constructed synteny blocks (common genomic blocks among all ingroup species). Because the size of the smallest genome in your case is 281Mbp (Tr), and so you cannot obtain synteny blocks with a total length exceeding 281Mbp with any smaller resolution.

In addition, if the genomes of your ingroup species are highly rearranged, it is difficult to concatenate the synteny blocks, which results in the generation of many APCFs.

On Jul 17, 2024, at 1:21 AM, jenny315 @.***> wrote:

Hello, Professor，

I have some questions about the result. Could you please give some stuggestion for me

My results are summarised below， when Block resolution is 50k, the result I got (form file APCF_size.txt) 609 APCFs total 228079891 bp. when Block resolution is 100K, the result I got (form file APCF_size.txt) 135 APCFs total 140661249 bp. when Block resolution is 300k, the result I got (form file APCF_size.txt) 56 APCFs total 64342708 bp.

My questions are summarised below,

I'm getting varied results with different resolutions, the amount and total length of APCFs are quite inconsistent. Is this normal? Maybe these results aren't usable at all. I know there can't be so many ancestral chromosomes (even up to 600). Therefore, I'm not sure which results to use. Even the biggest result obtained here (609 APCFs, comprising 228079891 bp) is still quite small (in comparison to the genome size of the species used). Is this normal? Or would you suggest me to adjust the parameters further? The genome size and chromosome number of the selected species are as follows, respectively： name sum_leh chr_num Ly 668,967,811 24 Cs 445,139,357 22 Dr 1,345,101,833 25 Gg 1,100,911,310 40 Lo 891,144,077 29 Lp 625,267,304 24 Ol 734,040,372 24 Tr 281,572,362 22 Species relationships and ancestor node settings@ marker are detailed in the files "config.SFs" and "tree.txt"

config.SFs

path of a net files

netdir /data/jenny/61MD5jenny/deschr/02spec/chainNet

path of a chain files

chaindir /data/jenny/61MD5jenny/deschr/02spec/chainNet

species-name tag1 tag2

tag1 (0: ref-species, 1: descendents, 2: outgroup)

tag2 (1: chromosome assembly, 0: others)

Warning for tag2: Use the value 1 only when a chromosome name starts with "chr".

species Ly 0 1 Cs 1 1 Dr 1 1 Gg 2 1 Lo 1 1 Lp 1 1 Ol 1 1 Tr 1 1

bLok resolution (bp): DO NOT CHANGE

resolution

tree.txt (((((((Ly:0.00582,Lp:0.01924):0.05216,Tr:0.12628):0.01846,Cs:0.13082):0.01913,Ol:0.12087):0.10993,Dr:0.1699):0.08193,Lo:0.13718)@:0.103875,Gg:0.120100); Many thanks, I appreciate your prompt response. Jenny

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[jenny315]

Hello, Professor, Thanks very much for your response.

• After deleting the smallest genome species, "TR", I still get similar results. When Block resolution is 50k, the result I got (form file APCF_size.txt) 622 APCFs total of 242508911 bp.
• • As we know from earlier studies, all of these species—aside from "LO"—experienced a WGD (Whole Genome Duplication) in comparison to the hypothesized ancestor(marker "@"), the node where this event took place is indicated by a "!" marker below. Did this incident affect the program's running results?

    ((((((Ly:0.00582,Lp:0.01924):0.07107,Cs:0.13082):0.01913,Ol:0.12087):0.10993,Dr:0.1699):!0.08193,Lo:0.13718)@:0.103875,Gg:0.120100);

    Many thanks, I appreciate your prompt response. Jenny

[jkimlab]

That means the amount of common genomic regions among the remaining species is about 242Mbp. If you want to increase the amount, you need to find and remove more genomes of species that can’t be aligned well against your reference.

On Jul 17, 2024, at 1:10 PM, jenny315 @.***> wrote:

Hello, Professor, Thanks very much for your response.

After deleting the smallest genome species, "TR", I still get similar results. When Block resolution is 50k, the result I got (form file APCF_size.txt) 622 APCFs total of 242508911 bp. As we know from earlier studies, all of these species—aside from "LO"—experienced a WGD (Whole Genome Duplication) in comparison to the hypothesized ancestor(marker "@"), the node where this event took place is indicated by a "!" marker below. Did this incident affect the program's running results? ((((((Ly:0.00582,Lp:0.01924):0.07107,Cs:0.13082):0.01913,Ol:0.12087):0.10993,Dr:0.1699):!0.08193,Lo:0.13718)@:0.103875,Gg:0.120100); Many thanks, I appreciate your prompt response. Jenny

— Reply to this email directly, view it on GitHub https://github.com/jkimlab/DESCHRAMBLER/issues/26#issuecomment-2232350674, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PV5MSQAXBLF5CA4PKS3ZMXVENAVCNFSM6AAAAABK65ZOQ2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZSGM2TANRXGQ. You are receiving this because you commented.

[jenny315]

Ok, thanks, I will explore further.