Does four gene match enough make a conclusion?

[zckoo007]

Hi Alessio，I move a new question here,
I ran all bins and found that two bins were matched, one is bin.unbinned.fa another is bin.592.fa,but only four gene match. the following code is the details

[ckzhu@vm-login01 mOTU_v2]$ grep "12476" job*
job1380.o1805966:COG0552_110	99.1	NA Clostridiales species incertae sedis@meta_mOTU_v25_12476
job926.o1805504:Consensus mOTUs: meta_mOTU_v25_12476
job926.o1805504:COG0172_1	99.9	NA Clostridiales species incertae sedis@meta_mOTU_v25_12476
job926.o1805504:COG0533_1	99.9	NA Clostridiales species incertae sedis@meta_mOTU_v25_12476
job926.o1805504:COG0215_1	99.9	NA Clostridiales species incertae sedis@meta_mOTU_v25_12476
job926.o1805504:COG0018_1	99.5	NA Clostridiales species incertae sedis@meta_mOTU_v25_12476

• less job926.o1805504

Extract genes
Map genes to mOTUs database
[E::main] Error: failed to save the marker genes sequences
Find taxonomy

RESULT:
Fasta sequence: bin.592.fa
Consensus NCBI ID: NA
Consensus taxonomy: Clostridiales species incertae sedis
Consensus mOTUs: meta_mOTU_v25_12476

Annotation: Consistent
Confidence: 97%

Number of detected genes: 4
Number of mapped genes: 4
Number of agreeing genes: 4
Percentage of agreeing genes: 100.0%

Gene annotation:
COG0172_1       99.9    NA Clostridiales species incertae sedis@meta_mOTU_v25_12476
COG0533_1       99.9    NA Clostridiales species incertae sedis@meta_mOTU_v25_12476
COG0215_1       99.9    NA Clostridiales species incertae sedis@meta_mOTU_v25_12476
COG0018_1       99.5    NA Clostridiales species incertae sedis@meta_mOTU_v25_12476

Does four gene enough to make the decision that the bins is meta_mOTU_v25_12476?
If this bin is correct, how should I analyze this bin next? what other analysis should I do later? Would you please give me some advise?

# checkm about this bin,  Completeness is 66.43%   Contamination is 1.75%

bin.592               k__Bacteria (UID203)             5449        103            57         56    46     1    0    0   0       66.43            1.75

[AlessioMilanese]

Hi @zckoo007,

Sorry if if took so long to reply, but I did not receive any notification for this issue. Not sure why.

Does four gene enough to make the decision that the bins is meta_mOTU_v25_12476?

Well, I did some simulations and when I have 4 genes mapping and all 4 are agreeing; I am correct 97% of the time. It means that when I simulated 100 genomes with only 4 genes mapping and 4 agreeing, 97 are correctly assigned. (it's a little more complicated than that, but that's the message).

If this bin is correct, how should I analyze this bin next? what other analysis should I do later? Would you please give me some advise?

The tool classify-genomes allow you to map genomes or MAGs or bins to the taxonomy used in mOTUs (https://github.com/motu-tool/mOTUs_v2). Basically it gives a taxonomic annotation to your bins. What type of analysis you want to do after depends on you and on the project. You could visualize a phylogenetic tree of the bins or check which MAGs are enriched in one state or the other (for example if you compare cases and controls). But for your evaluations, you now know that your bin/MAG belong to the order Clostridiales.