Thank you in advance!
I’m trying to use the lefse plot to identify bugs that have a significantly different relative abundance between a disease group and a healthy control group, and then from there use the relative abundance to see if there are any significant differences in relative abundance using the nonrarefied data between patients with specific symptoms vs without those symptoms within the disease group.
I have a file that underwent the following command:
format_input.py exported_202010261223/otu_table_w_tax.txt.for.lefse.tsv exported_202010261223/otu_table_w_tax.txt.lefse.in -c 1 -u 2 -o 1000000
and the .in file spits out 32 entries of numbers beneath each bug name, I presume corresponding to the 32 samples. However, I’m not sure how to tell if these are the raw number of reads that bug had for that sample, or what order the samples are in, or if this is rarefied or non-rarefied.
Would somebody be able to help me figure out how to interpret the .in file from this format?