Gene order display option for custom extraction #30
Comments
biomguler
changed the title
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I am working on a trial version of PhyloSuite, it contains your required functions, if you are interested, I can send it to you. |
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Dear Zhang,
It would be very nice to get an updated version of your software.
…------
Murat Güler
_______________________________________________________
Ph.D. Student | Genomic Epidemiology Group (C055)
German Cancer Research Center | Deutsches Krebsforschungszentrum (DKFZ)
Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
Phone: +49 1575 227 04 51
http://www.dkfz.de/en/genomische-epidemiologie/
On Mon, Oct 25, 2021 at 2:34 PM zhang dong ***@***.***> wrote:
I am working on a trial version of PhyloSuite, it contains your required
functions, if you are interested, I can send it to you.
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What system do you use? Win 10? |
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Yes, I am using win 10.
…On Tue, Oct 26, 2021, 08:22 zhang dong ***@***.***> wrote:
What system do you use? Win 10?
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Ok, I will send a packaged version to you later. There are some minor places need fine adjustment. |
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Great, thanks!
…On Tue, Oct 26, 2021, 08:26 zhang dong ***@***.***> wrote:
Ok, I will send a packaged version to you later. There are some minor
places need fine adjustment.
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Could you send me your email address? |
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Sure, here it is.
***@***.***
…On Tue, Oct 26, 2021, 10:00 zhang dong ***@***.***> wrote:
Could you send me your email address?
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I don't know why i will try to solve if you still unable to send.
…On Tue, Oct 26, 2021, 10:22 zhang dong ***@***.***> wrote:
[image: image]
<https://user-images.githubusercontent.com/15956921/138837126-d60ebf8f-ff68-47c3-a0d1-6f41acfe7919.png>
seems your email address was masked?
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maybe you can send me a screenshot of your email |
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Sure, here it is.
…On Tue, Oct 26, 2021, 10:29 zhang dong ***@***.***> wrote:
maybe you can send me a screenshot of your email
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Dear Murat,
The attachment file is the trial version of PhyloSuite, which contains
several functions you want:
1. it can customize the gene list you want to extract via "Add row"
button in "Genes" tab
of extracter function.
2. it can draw RSCU figure directly without R, however,
I suspect that your RSCU problem might be caused by a bad input file, so
I am not sure this new function will resolve your problem. If the
problem persists, you may send your data to me to debug the problem..
3. I added a "Draw gene order" function under Mitogenome menu, it
takes "linear_order.txt" file (available in "files" folder of the
results) as input to draw gene order figure. Please note that you need
to extract the data anew to generate that file using this new version,
as the format of this file has been changed.
By the way, this version of PhyloSuite is still under development
(codonW function is not finished),
so it may contain bugs. Please check your results carefully and
contact me if you encounter a problem
.
Sincerely,
Dong
PhyloSuite_v1.2.2_Win_beta.rar
<https://drive.google.com/file/d/1Sthsi0LJKWytVM8nozor5gE80Mn8-UA7/view?usp=drive_web>
bio-mguler ***@***.***> 于2021年10月26日周二 下午4:40写道：
… Sure, here it is.
On Tue, Oct 26, 2021, 10:29 zhang dong ***@***.***> wrote:
> maybe you can send me a screenshot of your email
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <
#30 (comment)
>,
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Dear Dong,
Thank you for the software. I need accession permission.
Best regards.
Murat.
------
Murat Güler
…_______________________________________________________
Ph.D. Student | Genomic Epidemiology Group (C055)
German Cancer Research Center | Deutsches Krebsforschungszentrum (DKFZ)
Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
Phone: +49 1575 227 04 51
http://www.dkfz.de/en/genomische-epidemiologie/
On Tue, Oct 26, 2021 at 12:47 PM zhang dong ***@***.***>
wrote:
Dear Murat,
The attachment file is the trial version of PhyloSuite, which contains
several functions you want:
1. it can customize the gene list you want to extract via "Add row"
button in "Genes" tab
of extracter function.
2. it can draw RSCU figure directly without R, however,
I suspect that your RSCU problem might be caused by a bad input file, so
I am not sure this new function will resolve your problem. If the
problem persists, you may send your data to me to debug the problem..
3. I added a "Draw gene order" function under Mitogenome menu, it
takes "linear_order.txt" file (available in "files" folder of the
results) as input to draw gene order figure. Please note that you need
to extract the data anew to generate that file using this new version,
as the format of this file has been changed.
By the way, this version of PhyloSuite is still under development
(codonW function is not finished),
so it may contain bugs. Please check your results carefully and
contact me if you encounter a problem
.
Sincerely,
Dong
PhyloSuite_v1.2.2_Win_beta.rar
<
https://drive.google.com/file/d/1Sthsi0LJKWytVM8nozor5gE80Mn8-UA7/view?usp=drive_web
>
bio-mguler ***@***.***> 于2021年10月26日周二 下午4:40写道：
> Sure, here it is.
>
>
> On Tue, Oct 26, 2021, 10:29 zhang dong ***@***.***> wrote:
>
> > maybe you can send me a screenshot of your email
> >
> > —
> > You are receiving this because you are subscribed to this thread.
> > Reply to this email directly, view it on GitHub
> > <
>
#30 (comment)
> >,
> > or unsubscribe
> > <
>
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> > .
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> >
> > or Android
> > <
>
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> >.
> >
> >
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I authorized, did you access to it?
bio-mguler ***@***.***> 于2021年10月26日周二 下午7:13写道：
… Dear Dong,
Thank you for the software. I need accession permission.
Best regards.
Murat.
------
Murat Güler
_______________________________________________________
Ph.D. Student | Genomic Epidemiology Group (C055)
German Cancer Research Center | Deutsches Krebsforschungszentrum (DKFZ)
Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
Phone: +49 1575 227 04 51
http://www.dkfz.de/en/genomische-epidemiologie/
On Tue, Oct 26, 2021 at 12:47 PM zhang dong ***@***.***>
wrote:
> Dear Murat,
>
> The attachment file is the trial version of PhyloSuite, which contains
> several functions you want:
>
> 1. it can customize the gene list you want to extract via "Add row"
> button in "Genes" tab
> of extracter function.
> 2. it can draw RSCU figure directly without R, however,
> I suspect that your RSCU problem might be caused by a bad input file, so
> I am not sure this new function will resolve your problem. If the
> problem persists, you may send your data to me to debug the problem..
> 3. I added a "Draw gene order" function under Mitogenome menu, it
> takes "linear_order.txt" file (available in "files" folder of the
> results) as input to draw gene order figure. Please note that you need
> to extract the data anew to generate that file using this new version,
> as the format of this file has been changed.
>
> By the way, this version of PhyloSuite is still under development
> (codonW function is not finished),
> so it may contain bugs. Please check your results carefully and
> contact me if you encounter a problem
> .
>
> Sincerely,
>
> Dong
> PhyloSuite_v1.2.2_Win_beta.rar
> <
>
https://drive.google.com/file/d/1Sthsi0LJKWytVM8nozor5gE80Mn8-UA7/view?usp=drive_web
> >
>
>
> bio-mguler ***@***.***> 于2021年10月26日周二 下午4:40写道：
>
> > Sure, here it is.
> >
> >
> > On Tue, Oct 26, 2021, 10:29 zhang dong ***@***.***> wrote:
> >
> > > maybe you can send me a screenshot of your email
> > >
> > > —
> > > You are receiving this because you are subscribed to this thread.
> > > Reply to this email directly, view it on GitHub
> > > <
> >
>
#30 (comment)
> > >,
> > > or unsubscribe
> > > <
> >
>
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> > >
> > > .
> > > Triage notifications on the go with GitHub Mobile for iOS
> > > <
> >
>
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> > >
> > > or Android
> > > <
> >
>
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> > >.
> > >
> > >
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub
> > <
>
#30 (comment)
> >,
> > or unsubscribe
> > <
>
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> >
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> > <
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> >
> > or Android
> > <
>
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> >.
> >
> >
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Yes, but I have a problem opening rar file.
[image: image.png]
------
Murat Güler
…_______________________________________________________
Ph.D. Student | Genomic Epidemiology Group (C055)
German Cancer Research Center | Deutsches Krebsforschungszentrum (DKFZ)
Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
Phone: +49 1575 227 04 51
http://www.dkfz.de/en/genomische-epidemiologie/
On Tue, Oct 26, 2021 at 1:52 PM zhang dong ***@***.***> wrote:
I authorized, did you access to it?
bio-mguler ***@***.***> 于2021年10月26日周二 下午7:13写道：
> Dear Dong,
> Thank you for the software. I need accession permission.
>
> Best regards.
> Murat.
> ------
>
> Murat Güler
> _______________________________________________________
> Ph.D. Student | Genomic Epidemiology Group (C055)
> German Cancer Research Center | Deutsches Krebsforschungszentrum (DKFZ)
> Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
> Phone: +49 1575 227 04 51
> http://www.dkfz.de/en/genomische-epidemiologie/
>
>
>
> On Tue, Oct 26, 2021 at 12:47 PM zhang dong ***@***.***>
> wrote:
>
> > Dear Murat,
> >
> > The attachment file is the trial version of PhyloSuite, which contains
> > several functions you want:
> >
> > 1. it can customize the gene list you want to extract via "Add row"
> > button in "Genes" tab
> > of extracter function.
> > 2. it can draw RSCU figure directly without R, however,
> > I suspect that your RSCU problem might be caused by a bad input file,
so
> > I am not sure this new function will resolve your problem. If the
> > problem persists, you may send your data to me to debug the problem..
> > 3. I added a "Draw gene order" function under Mitogenome menu, it
> > takes "linear_order.txt" file (available in "files" folder of the
> > results) as input to draw gene order figure. Please note that you need
> > to extract the data anew to generate that file using this new version,
> > as the format of this file has been changed.
> >
> > By the way, this version of PhyloSuite is still under development
> > (codonW function is not finished),
> > so it may contain bugs. Please check your results carefully and
> > contact me if you encounter a problem
> > .
> >
> > Sincerely,
> >
> > Dong
> > PhyloSuite_v1.2.2_Win_beta.rar
> > <
> >
>
https://drive.google.com/file/d/1Sthsi0LJKWytVM8nozor5gE80Mn8-UA7/view?usp=drive_web
> > >
> >
> >
> > bio-mguler ***@***.***> 于2021年10月26日周二 下午4:40写道：
> >
> > > Sure, here it is.
> > >
> > >
> > > On Tue, Oct 26, 2021, 10:29 zhang dong ***@***.***> wrote:
> > >
> > > > maybe you can send me a screenshot of your email
> > > >
> > > > —
> > > > You are receiving this because you are subscribed to this thread.
> > > > Reply to this email directly, view it on GitHub
> > > > <
> > >
> >
>
#30 (comment)
> > > >,
> > > > or unsubscribe
> > > > <
> > >
> >
>
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> > > >
> > > > .
> > > > Triage notifications on the go with GitHub Mobile for iOS
> > > > <
> > >
> >
>
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> > > >
> > > > or Android
> > > > <
> > >
> >
>
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> > > >.
> > > >
> > > >
> > >
> > > —
> > > You are receiving this because you commented.
> > > Reply to this email directly, view it on GitHub
> > > <
> >
>
#30 (comment)
> > >,
> > > or unsubscribe
> > > <
> >
>
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> > >
> > > .
> > > Triage notifications on the go with GitHub Mobile for iOS
> > > <
> >
>
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> > >
> > > or Android
> > > <
> >
>
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> > >.
> > >
> > >
> >
> > —
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>
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use the software "WinRAR" to unpack it.
bio-mguler ***@***.***> 于2021年10月26日周二 下午7:56写道：
… Yes, but I have a problem opening rar file.
[image: image.png]
------
Murat Güler
_______________________________________________________
Ph.D. Student | Genomic Epidemiology Group (C055)
German Cancer Research Center | Deutsches Krebsforschungszentrum (DKFZ)
Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
Phone: +49 1575 227 04 51
http://www.dkfz.de/en/genomische-epidemiologie/
On Tue, Oct 26, 2021 at 1:52 PM zhang dong ***@***.***> wrote:
> I authorized, did you access to it?
>
> bio-mguler ***@***.***> 于2021年10月26日周二 下午7:13写道：
>
> > Dear Dong,
> > Thank you for the software. I need accession permission.
> >
> > Best regards.
> > Murat.
> > ------
> >
> > Murat Güler
> > _______________________________________________________
> > Ph.D. Student | Genomic Epidemiology Group (C055)
> > German Cancer Research Center | Deutsches Krebsforschungszentrum (DKFZ)
> > Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
> > Phone: +49 1575 227 04 51
> > http://www.dkfz.de/en/genomische-epidemiologie/
> >
> >
> >
> > On Tue, Oct 26, 2021 at 12:47 PM zhang dong ***@***.***>
> > wrote:
> >
> > > Dear Murat,
> > >
> > > The attachment file is the trial version of PhyloSuite, which
contains
> > > several functions you want:
> > >
> > > 1. it can customize the gene list you want to extract via "Add row"
> > > button in "Genes" tab
> > > of extracter function.
> > > 2. it can draw RSCU figure directly without R, however,
> > > I suspect that your RSCU problem might be caused by a bad input file,
> so
> > > I am not sure this new function will resolve your problem. If the
> > > problem persists, you may send your data to me to debug the problem..
> > > 3. I added a "Draw gene order" function under Mitogenome menu, it
> > > takes "linear_order.txt" file (available in "files" folder of the
> > > results) as input to draw gene order figure. Please note that you
need
> > > to extract the data anew to generate that file using this new
version,
> > > as the format of this file has been changed.
> > >
> > > By the way, this version of PhyloSuite is still under development
> > > (codonW function is not finished),
> > > so it may contain bugs. Please check your results carefully and
> > > contact me if you encounter a problem
> > > .
> > >
> > > Sincerely,
> > >
> > > Dong
> > > PhyloSuite_v1.2.2_Win_beta.rar
> > > <
> > >
> >
>
https://drive.google.com/file/d/1Sthsi0LJKWytVM8nozor5gE80Mn8-UA7/view?usp=drive_web
> > > >
> > >
> > >
> > > bio-mguler ***@***.***> 于2021年10月26日周二 下午4:40写道：
> > >
> > > > Sure, here it is.
> > > >
> > > >
> > > > On Tue, Oct 26, 2021, 10:29 zhang dong ***@***.***> wrote:
> > > >
> > > > > maybe you can send me a screenshot of your email
> > > > >
> > > > > —
> > > > > You are receiving this because you are subscribed to this thread.
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> > >
> >
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Hi,
I have a problem with analyzing the mitogenome of 20 amoeba species. Because I have multiple issues, I listed them below.
The species have different genome structures than animal mitogenomes, mitogenomes contain fusion cox1 and cox2, rps, and rpl genes. I am trying to extract genes. When I choose differently than the "mitogenome" option, the gene order display screen is disappearing. So, I can't modify options. It results in losing some gene data in the itol gene order file (only contain default listed genes). Also, the "geneStat.cvs" file doesn't show these genes. How can I customize the gene list without losing the results; that I get when using the "mitogenome" extraction parameter?
I am also trying to get RSCU plots. I can draw graf when I use a single mitogenome, but not with multiple. When I run the R script I get the error below.
Error: Aesthetics must be either length 1 or the same as the data (62): x and fill
Note: I get information from the paper; that mentions mapping gene orders onto the tree and other features that I want to get only for the mitogenome extraction option. I am trying to find alternative solutions.
The text was updated successfully, but these errors were encountered: