Open your Terminal (find in your Utilities folder in your Applications). If you have any troubles with input files with Qiime, check to make sure that files are saved with Unix (LF) Line breaks and Encoding with Unicode (UTF-8), and that there are no hidden endings on your file. Here’s one the first of ~6,000,000 google hits for “unix tutorial”: Īlso, you will want to have a good text editor to view, edit, and check your files.
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There are plenty of great free online tutorials to help you out. This may sound intimidating, but if you take a few hours to learn some basic operations in your Unix/Linux/Terminal, it will save you *LOTS* of time and frustration in the future. QIIME and other bioinformatic programs work with through Unix command line interface. Greg Bonito kindly prepared a Qiime cheat sheet that you can use in addition to the Qiime tutorial that’s on line….īefore we get started, there are some things you should know… Please send your powerpoints to Emily by noon on Thursday. Pick your bacteria and tell us about its morphology, phylogeny and ecology. On Thursday you will each give us a 5 minute presentation on a bacteria from our set of class cultures. Add 10 μL of your culture suspension to each prepared wellįinally – start a broth culture by putting a sterile loop sample of your pure culture into culture broth. In rows 1-3 prepare a dilution sequence of 3 different antibiotics. Then – prepare a 96 well plate by adding 100 μL culture broth to all wells.Īdd an additional 100 μL to lanes 1 and 2 only When plate is dry dispense antibiotic disks onto the new culture plate. Plate 100 μL of this pure culture suspension onto a fresh culture plate using sterile technique, spread with glass spreading rod. Everyone chooses a bacteria and does the following.įirst, prepare a suspension of your culture in 500 μL sterile water. In class today you are looking for variation in antimicrobial resistance across your pure cultures. 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. 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.Īs 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.
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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. 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 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”. Okay – hopefully you all managed to work your way through Qiime in some form or another.