Entering edit mode
6.6 years ago
a.alsayed.phd
▴
10
Hello, I have OTUs (from 16 s microbiome analysis - MIseq) on excel sheets for many samples. I would like to plot the relative abundance of each species in a graph. I am new to this field, so please, can anyone advise me how to do that? Many Thanks
This is a question, not a tool post, so I have updated your post.
But it's not clear from your question whether you are trying to calculate the relative abundance from reads, or whether you already know the abundance and are just trying to plot it. Can you clarify?
Thank you for your reply I laready know the abundance for each OTU and I am trying to know the relative abundance and plot it.
If you already have the abundance data in Excel... then this is not really a bioinformatics question. Generally, you go to the "Insert" tab, draw a rectangle around the data, select "Column" and pick a chart type.
Try this for more information:
https://blog.hubspot.com/marketing/how-to-build-excel-graph
Thank you for your advise I know, but I have around 137 rows, 3 examples (OTU ID) as following: k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Micrococcaceae;g__Rothia k__Bacteria;p__Fusobacteria;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium
and I am not sure how to compare each species individually? so not the combinations comparison
This sounds like a problem needing a customized solution. I think you need to talk to the bioinformatician working with you...