Comments (3)
cfrioux
commented on May 27, 2024
Hi,
Genbank format
If you use reference genomes, e.g. from the NCBI, you can download genbank files directly on the database. Be sure to pick ones that contain annotations, or otherwise reannotate them.
Prokka is an annotation tool that provides genbank files.
Otherwise, if you use genomes that you annotated with Eggnog-mapper, you might want to take a look to emapper2gbk.
SBML format
The format is very usual in metabolic modelling. Carveme, gapseq and ModelSEED will provide SBMLs.
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LiZhihua1982
commented on May 27, 2024
Dear Prof.Clémence Frioux,
Thank you very much for your explain! For example, I have several MAGs, I want to analyze them using metage2metabo, first I need prepare gdb file using prokka, which I found it will report error when direct using prokka, it need revise the taxid and LOCUS line, this will need a large time when many MAGs need to be revised. second, I need prepare the seed file. If possible, would you take the MAGs as input file directly. Thanks again!
Best regards
Li Zhihua
…________________________________
发件人: Clémence Frioux ***@***.***>
发送时间: 2023年8月21日 14:15
收件人: AuReMe/metage2metabo ***@***.***>
抄送: Li Zhihua ***@***.***>; Author ***@***.***>
主题: Re: [AuReMe/metage2metabo] How to prepare inputs for metage2metabo (Issue #51)
Hi,
Genbank format
If you use reference genomes, e.g. from the NCBI, you can download genbank files directly on the database. Be sure to pick ones that contain annotations, or otherwise reannotate them.
Prokka is an annotation tool that provides genbank files.
Otherwise, if you use genomes that you annotated with Eggnog-mapper, you might want to take a look to emapper2gbk<https://github.com/AuReMe/emapper2gbk>.
SBML format
The format is very usual in metabolic modelling. Carveme, gapseq and ModelSEED will provide SBMLs.
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Reply to this email directly, view it on GitHub<#51 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AJI2BJLEPWMZM4LSSMECFBDXWL4H7ANCNFSM6AAAAAA3XDPGGY>.
You are receiving this because you authored the thread.Message ID: ***@***.***>
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cfrioux
commented on May 27, 2024
If you want help in generating the seed file, take a look at the documentation. You can use a [dedicated command[(https://metage2metabo.readthedocs.io/en/latest/command.html#m2m-seeds) to generate the SBML.
We do not take the MAGs directly as users might want to use their favourite annotation software.
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Related Issues (20)
- Hi
- Hi，I'm trying to run your pipeline but I had an error. Do you have any idea how can I solve this? I'm leaving here the input and outputs.Thank you very much
- Progress problem HOT 4
- I'm terribly sorry, but I can't solve it by trying many methods. I'm looking for your help.
- A few process questions HOT 4
- I have the following problems when running the t2d_m2m_target_producers.R file: HOT 8
- Multiple errors when running test data HOT 7
- A better focus on the host metabolism when a host is provided HOT 1
- Issue with pathway tools API limitation and PGDB entries verification HOT 4
- Compute deadend and orphan metabolites
- Non optimal powergraph visualisation HOT 2
- m2m_analysis powergraph not working as expected HOT 27
- m2m recon not working with gbff file inputs HOT 4
- Error with analysis graph when using taxon_id HOT 5
- CRITICAL:metage2metabo.m2m.reconstruction:Something went wrong running Pathway Tools. See the log file in /home/chencong/output3/pgdb_log/log_error.txt HOT 6
- No /home/chencong/.ncbirc file, please fix it before using the program HOT 5
- [Question] Where can I find seed files? HOT 4
- Install metage2metabo problem HOT 5
- mpwt could not find the version of Pathway Tools HOT 1
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