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jkimlab / mySyntenyPortal

A stand-alone application for constructing websites for visualizing and browsing synteny blocks
GNU General Public License v3.0
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How to generate synteny block files and sizes files? #16

Open vaishnaviannabhemoju opened 6 months ago

vaishnaviannabhemoju commented 6 months ago

This is a great work. I am wondering how I can generate synteny block files and sizes files for my genomes.

jkimlab commented 6 months ago

mySyntenyPortal can generate the synteny blocks internally if you just provide the assembly files. Please refer to the description of "Configuration file - With assembly sequences" in the readme file. And I don't think you need the size files.

vaishnaviannabhemoju commented 6 months ago

Thank you for your response. I attempted to use the example assembly sequences, but that doesn't seems to be working out. It is working perfectly for the synteny block definition conf file. What do you think might be the potential issue? I appreciate your time.

jongin333 commented 6 months ago

Hello, it's not clear what situation you're in just from the question alone. If you could provide any error messages that occurred during the installation or execution process, it would be helpful to understand the situation.

Thank you.

vaishnaviannabhemoju commented 6 months ago

Hi,

These are the sample errors I'm encountering.

Building synteny blocks
Making linear plot inputs
Making gene track inputs

My understanding is that that by providing the assembly files, the program should generate the synteny blocks files and sizes automatically. If you have any insights or suggestions on how to resolve the issue, please let me know. Your assistance is greatly appreciated.

Thank you.

jongin333 commented 6 months ago

Hello,

It seems that the message you've received is not an error message but rather an indication that there is no alignment between the assemblies or that synteny blocks cannot be generated.

If there are sufficiently similar regions between the assemblies you're trying to analyze synteny analysis, then there seems to be an issue starting from the step of creating synteny blocks.

To understand this issue better, it would be helpful if you could provide screenshots of the configuration file you've written and the command you've executed. This would assist in identifying the root cause.

Thank you.

vaishnaviannabhemoju commented 6 months ago

Thank you for your patience. Initially, I suspected that the issue might lie with my dataset, possibly due to the absence of synteny blocks. However, it seems that the provided command yields identical outputs for both my data and the example dataset. I have attached the configuration files(conf file.txt) and corresponding outputs for my dataset(cacao output.txt) and the example data(Example data output.txt) for your review. The command I am executing to build the site is: ./mySyntenyPortal build -conf configurations/sample.conf.

Example data output .txt cacao output .txt conf file.txt

jongin333 commented 6 months ago

Hi,

Based on the error messages provided in the file you sent, it seems that the third-party programs of mySyntenyPortal are not functioning properly.

Could you please confirm whether any errors occurred during the execution of the install command (perl ./install.pl build)?

If the installation completed successfully and you received the "Success!!" message, please verify if the programs within the path "src/third_party/[program names]" directory are functioning correctly.

Thank you.