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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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Issues of output results from riptide #147

Closed Xingchen-Bian closed 2 years ago

Xingchen-Bian commented 2 years ago

Dear Matt Jenior,

I'm using riptide for transcriptomic-constraint genome scale metabolic model. When I use different gene expression datasets, I got similar results, i.e. similar growth rate, flux distributions of each reactions. I do not know how to explain this. The model information are as follows: The model was constructed using carveme with cplex as its solver (https://carveme.readthedocs.io/en/latest/usage.html ). I use this code: carve 163560.faa -g LB -i LB. The no constraint model has 1028 genes. The gene expression datasets are from control group (ctrl_4h) and antibiotic combination treatment group (comb_4h). There are 197/1028 differentially expressed genes (adjusted p value <0.05, fold change >2). Here attached the bacteria genome annotation file 163560.faa (for model construction), the model LB163560 I've constructed, the gene expression data from two groups and output results from riptide.

I would be very grateful if you could help. Thank you very much!

Best regards, Xingchen Bian Attachments.zip

cdanielmachado commented 2 years ago

Hi, this looks like a problem with riptide, not CarveMe...

Xingchen-Bian commented 2 years ago

Thank you for your reply!

Kind regards, Xingchen Bian

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Xingchen Bian College of Pharmacy, Fudan University Huashan Hospital, Fudan University

12 Wulumuqi Zhong Rd, Shanghai, China

At 2021-11-04 14:17:01, "Daniel Machado" @.***> wrote:

Hi, this looks like a problem with riptide, not CarveMe...

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