Entering edit mode
2.9 years ago
serene.s
•
0
Hi Everyone! I am doing taxonomic analysis of metagenomics datasets/samples. I have use MetaPhlAn3 tool for that purpose so now I have a file that contains abundance of all the species of all samples in the excel format. But my goal is to find out top 25 species from all the samples.So, please suggest me any tool or standard process that can do it for me.
Thanks Saraswati
You can use pivot table utility in excel.
yes that can also be done although I have not tried that. The thing is I want to plot the abundance of top 25 species of 8 samples. so Do you think Pivot table would give top 25 of all samples that can be ploted on a stacked bar graph?
Why not?
Usually what I was doing for such representation earlier (before using R off course). I was creating a pivot table using Taxonomy (Genus/Species/....) as a Rows, Samples as a Column, and abundance as Values (each sample; I used to take average abundance here). Once the pivot table was ready I used to rank them based on sum of each taxa and then represent the top10/top20 (top25 in your case).