Hi all, thanks much for your inputs previously. I finally got all the analysis done and got all the data we needed (yeah!!!), e.g., classified OTU, alpha/beta diversity, rarefraction etc.
Although I got stuck with the step of making figures. For example, after classify.otu, I got xxx.tax.summary, xxx.taxonomy. and I’m supposed to generate something like a barplot to present the data. But here is my question:
- the xxx.taxonomy data looks like this
H9_9947 Bacteria(100);Firmicutes(91);Clostridia(90);Clostridiales(88);Ruminococcaceae(86);Oscillibacter(86);
H9_9801 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified;
H9_9740 Bacteria(100);Firmicutes(97);Clostridia(97);Clostridiales(97);Ruminococcaceae(97);unclassified;
H9_9721 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(99);
H9_9695 Bacteria(100);“Proteobacteria”(100);Betaproteobacteria(100);Burkholderiales(99);Sutterellaceae(89);unclassified;
H9_9625 Bacteria(100);“Bacteroidetes”(100);“Bacteroidia”(99);“Bacteroidales”(99);Bacteroidaceae(91);Bacteroides(91);
H9_958 Bacteria(100);“Bacteroidetes”(100);“Bacteroidia”(100);“Bacteroidales”(100);Bacteroidaceae(97);Bacteroides(97);
H9_9558 Bacteria(100);Firmicutes(81);unclassified;unclassified;unclassified;unclassified;
H9_9444 Bacteria(100);“Actinobacteria”(100);Actinobacteria(100);Actinomycetales(100);Microbacteriaceae(100);Leucobacter(100);
H9_9381 Bacteria(100);“Actinobacteria”(95);Actinobacteria(95);Coriobacteriales(94);Coriobacteriaceae(94);Collinsella(90);
H9_9359 Bacteria(100);unclassified;unclassified;unclassified;unclassified;unclassified;
H9_9187 Bacteria(100);Firmicutes(99);Clostridia(99);Clostridiales(99);Ruminococcaceae(95);Sporobacter(85);
H9_9146 Bacteria(100);Firmicutes(98);Clostridia(98);Clostridiales(96);unclassified;unclassified;
H9_9134 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Oscillibacter(90);
H9_9131 Bacteria(100);unclassified;unclassified;unclassified;unclassified;unclassified;
H9_9119 Bacteria(100);Firmicutes(82);unclassified;unclassified;unclassified;unclassified;
H9_9108 Bacteria(100);“Bacteroidetes”(100);“Bacteroidia”(100);“Bacteroidales”(100);Bacteroidaceae(100);Bacteroides(100);
H9_9060 Bacteria(100);“Bacteroidetes”(100);“Bacteroidia”(100);“Bacteroidales”(100);“Prevotellaceae”(100);Prevotella(96);
H9_8924 Bacteria(100);Firmicutes(100);Erysipelotrichia(100);Erysipelotrichales(100);Erysipelotrichaceae(100);Clostridium_XVIII(99);
H9_8888 Bacteria(100);“Bacteroidetes”(99);“Bacteroidia”(99);“Bacteroidales”(99);Bacteroidaceae(93);Bacteroides(93);
It’s my understanding that those OTUs were all belong to H9 (the individual). And I’m supposed to combine all the OTUs into each individuals. (?) But I really don’t know how to combine them, or should I at all?
- I looked up some similar questions, one kind fella suggested to sort xxx.tax.summary data based on which bacteria (e.g., e coli) and then generate chart. How can I make taxa summary plots in mothur
But I didn’t completely understand it. Would anyone shed some lights please?
My xxx.tax.summary data looks like this
taxlevel rankID taxon daughterlevels total H
0 0 Root 2 1819040 1819040
1 0.1 Archaea 2 28 28
2 0.1.1 Crenarchaeota 1 1 1
3 0.1.1.1 Thermoprotei 1 1 1
4 0.1.1.1.6 unclassified 1 1 1
5 0.1.1.1.6.1 unclassified 1 1 1
6 0.1.1.1.6.1.1 unclassified 0 1 1
2 0.1.2 Euryarchaeota 1 27 27
3 0.1.2.4 Methanobacteria 1 27 27
4 0.1.2.4.1 Methanobacteriales 1 27 27
5 0.1.2.4.1.1 Methanobacteriaceae 1 27 27
6 0.1.2.4.1.1.2 Methanobrevibacter 0 27 27
1 0.2 Bacteria 23 1819012 1819012
2 0.2.1 Acidobacteria 7 14 14
3 0.2.1.1 Acidobacteria_Gp1 1 3 3
4 0.2.1.1.1 Acidobacteria_Gp1_order_incertae_sedis 1 3 3
5 0.2.1.1.1.1 Acidobacteria_Gp1_family_incertae_sedis 1 3 3
6 0.2.1.1.1.1.1 Gp1 0 3 3
3 0.2.1.8 Acidobacteria_Gp16 1 1 1
4 0.2.1.8.1 Acidobacteria_Gp16_order_incertae_sedis 1 1 1
5 0.2.1.8.1.1 Acidobacteria_Gp16_family_incertae_sedis 1 1 1
6 0.2.1.8.1.1.1 Gp16 0 1 1
3 0.2.1.12 Acidobacteria_Gp2 1 4 4
4 0.2.1.12.1 Acidobacteria_Gp2_order_incertae_sedis 1 4 4
5 0.2.1.12.1.1 Acidobacteria_Gp2_family_incertae_sedis 1 4 4
6 0.2.1.12.1.1.1 Gp2 0 4 4
3 0.2.1.15 Acidobacteria_Gp22 1 1 1
4 0.2.1.15.1 Acidobacteria_Gp22_order_incertae_sedis 1 1 1
5 0.2.1.15.1.1 Acidobacteria_Gp22_family_incertae_sedis 1 1 1
6 0.2.1.15.1.1.1 Gp22 0 1 1
3 0.2.1.20 Acidobacteria_Gp3 1 2 2
4 0.2.1.20.1 Acidobacteria_Gp3_order_incertae_sedis 1 2 2
5 0.2.1.20.1.1 Acidobacteria_Gp3_family_incertae_sedis 1 2 2
6 0.2.1.20.1.1.1 Gp3 0 2 2
3 0.2.1.21 Acidobacteria_Gp4 1 2 2
4 0.2.1.21.1 Acidobacteria_Gp4_order_incertae_sedis 1 2 2
5 0.2.1.21.1.1 Acidobacteria_Gp4_family_incertae_sedis 1 2 2
6 0.2.1.21.1.1.1 Gp4 0 2 2
) works. If representing a group of subjects, box plots work – I’ve done that. I go into the tax file, pull out my groupings, summarize in my favorite graphics program, and go from there.