After our analyses are finished we will send most users just two files. The first file is the report file that quantifies the percentage of all sequences that were found for each OTU (operational taxonomic unit) for each sample. The second is a library file that lists the species that match to the OTU.
The first file will be the break down of the relative number of OTU’s in each sample. This is called the report file.
The report file will have one column for the OTU ID. The subsequent columns will be the number of sequences of the different OTU’s in each sample. The column header will be the sample ID of the vial that you had placed the sample in.
Here is a sample portion of a report:
To get the relative abundances, you just need to divide each cell by the column sum:
In this above example, 4 OTU’s are listed. For the first sample (S0001), 43.31% of the sequences were of OTU ID #1 and 0.18% were of OTU ID #2. In contrast, for sample S0002, 48.44% were of OTU ID #1 and 46.88% were of OTU ID #2. Note, in report files, these percentages will always sum to 1 in a column.
Library matching file
The library matching file will look something like this…
The first column is OTU ID. This is the identification number of the OTU that you will use to match OTU’s in your data file.
The second column are the species in our library that match or closely match with the OTU.
In the above example, OTU 1 has species in 4 species that match with OTU1.
To use these files to interpret your data, you start with the OTU ID in the data file and then use this library file as reference. If a particular sequence is matched with OTU ID #1, then it is likely either species of the genus Brachyglottis and/or Saussurea. Note the species could be from a different genus that is not in our library but is closely related.
If you want to manually examine the matching of sequences and species, you will have to manually query a database to find the best match. To do this, go to the FASTA (pronounced FAST-AY) file (with the suffix .fna). Find the OTU ID in question. Copy the sequence next to it. Go to http://blast.ncbi.nlm.nih.gov/Blast.cgi. Select nucleotide blast. Paste the OTU sequence in the box where it asks for the FASTA sequence. Hit BLAST.