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Dear Professor
Could you please provide the relevant input files in the 00.rawData folder where the input files in the website(https://github.com/GRONINGEN-MICROBIOME-CENTRE/Groningen-Microbiome/blob/master/Projects/SV_BA/s01.Data_cleaning.Rmd) are located, or could you please tell me how to get them?Or give me a sample file.
I've got the file of "dsgv.csv","vsgv.csv" and "representatives.genomes.taxonomy.csv".
I don't know how to get "s02.dSVs_anno.tsv", "s03.vSVs_anno.tsv", "Species_genome_size.tsv“， ”NCBI_accession.txt“， ”progenome1_species_relationship.tsv“, ”LLD.s1135.SV_spe_abun.S.tsv“，”300OB.s298.SV_spe_abun.S.tsv“

                                                                                                                                          Looking forward to your reply. 

Hi,

I followed the SV_pipeline (https://github.com/GRONINGEN-MICROBIOME-CENTRE/Groningen-Microbiome/tree/master/Scripts/SV_pipeline) to practice, and the entire pipeline was completed. But the two final results dsgv.csv and vsgv.csv were empty.

Maybe you can help upload an example of the final result?
I want to see what the final result looks like and is it the result I expected.

If you can help, thank you very much.

best
wanjin.hu

Nice to meet you, Lianmin Chen.

I am a student in Fudan University and new to microbiological network inference. I have read the paper Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity carefully. I still couldn't understand the paragraph:

Co-occurrence network inference: presence and absence of each bacterial species and metabolic pathway were treated as binary traits. The pair-wise co-occurrence relationship between two microbial factors (species or pathway) in each cohort was assessed using Pearson’s chi-squared test. If the number of co-occurrence pairs was greater than the number of co-exclusion pairs, the two microbial factors were considered to be a co-occurrence. If the number of co-occurrence pairs was less than the number co-exclusion pairs, the two factors were considered to be a co-exclusion. Permutation (100×) was conducted to determine significance at an FDR < 0.05. In each permutation, the presence and absence of each microbial factor was randomly shuffled across samples.

And this section is not explained enough in the code. Could you provide more information or some example? Thank you very much!

My questions were that:
(1)How do you integrate the results of SparCC and SpiecEasi ? Take the intersection directly?
(2)How to define and calculate co-occurrence pairs and co-exclusion pairs?
(3)There are many network inference strategies. Bin Ma et al. Microbiome(2020) and Gipsi Lima-Mendez et al. Sicence(2015)
adopt another kind of microbiological network inference strategy. What kind of network inference is better?

My e-mail is [email protected]. If it's convenient for you, we can talk about the question more. Thank you.

Best wishes to you.

Longhao Jia

Dear Groningen Microbiome Team,