Folks
okay – hopefully you all managed to work your way through Qiime in some form or another. If so, you will have generated a file within your data folder called “otus” and within that folder there will be a file called “otu_table.txt”. You can open that table in excel and see that you have the # of reads for each sequence by sample and the last column in that sheet shows the identification of the sequence. If you haven’t been able to get this far – you can go to our class folder (go to “assignments” tab and click on “class library” link) and download an excel spreadsheet that you will find there in Qiime Folder/duke454_wang_080511/otus/Organized_OTU_Table. Here I have already organized the data in order of sample ID and on the 2nd tab have counted the unique OTUs by sample ID.
As your assignment for our first class after spring break, you should explore this data together with potential environmental correlates (see “Qiime Folder/duke454_wang_080511/Environmental Data from Streans”) of samples JW1-JW35 to answer a question. You can either devise your own question OR by default, find out if there is any correlation between the extent of watershed development and the OTU richness (=# unique OTUs) across these 35 streams.
Good luck!
