Getting Acquainted with Data/QIIME interface

Andrew and I met at approximate 9:27PM to start exploring the QIIME online interface and get a better feel of the data that is generated by QIIME (http://www.microbio.me/qiime/). We were able to download a .jnlp file after doing a test meta analysis and this file contains an OTU table.

Using the tutorial here (http://www.microbio.me/qiime/docs/tutorials/tutorial.html), I was able to figure out how to upload metadata. It entails choosing different MIMARKS compliant fields then generating a template. This is downloaded as a zip and has three files: field reference (information about the different fields and what you can actually input. ex Y/N or [text]), prep_template, and sample_template.

The prep_template and sample_template must be saved in the .TXT (tab delimited) format. In order to upload onto QIIME web-based interface, the two files must have the two files.

After doing a test meta analysis, I downloaded the zip archive and cut/paste the information from meta_analysis_tmpyoeE07rp6FgSBwGn4VnM_map.txt file into Excel. I later cut and paste appropriate information from this file into the prep_template and sample_template generated earlier. I data such as BASE %BF AVE (from the meta data file we have) into the sample_template. Fields (column names) must have only a-z characters and numbers (NO SPACES).

The upload of a zip of these two files was completed with a few fixable message errors (changing the field names so that they were lower case or removed spaces from the field names). Another upload of the zip went through. However the sample names I took from the metadata do not seem to match whatever is already on the website. After successful upload, QIIME asks me if I want to overwrite the current file because the names differ.

Questions to ask in tomorrow’s lab meeting:

  • What sample names should we be using?
  • Where are the meta data after baseline measurements?
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Posted in Andrew, Keiko | Leave a comment

Meeting with Dr. Lamendella

Goals
Determined location of OTU table.
Meta analysis>input name>perform analysis>find “dietary crossover”

TO DO:

  • Add data after baseline.
  • Upload metadata, format into qiime.
  • Search qiime database to learn how to deal with database
  • How to convert .biome file to .xls or .csv
Posted in Andrew, Keiko | Leave a comment

Tutorial for QIIME

http://qiime.org/tutorials/tutorial.html

This tutorial explains how to use the QIIME (Quantitative Insights Into Microbial Ecology) Pipeline to process data from high-throughput 16S rRNA sequencing studies. If you have not already installed qiime, please see the section Installing Qiime first. The purpose of this pipeline is to provide a start-to-finish workflow, beginning with multiplexed sequence reads and finishing with taxonomic and phylogenetic profiles and comparisons of the samples in the study. With this information in hand, it is possible to determine biological and environmental factors that alter microbial community ecology in your experiment.

Here is a short/free article about advantages of QIIME.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3156573/?tool=pubmed

 

 

 

Posted in Keiko | Leave a comment

First meeting

  • Attempted to install VirtualBox and QIIME, but need adminstrative access.
  • Set up blog to keep track of shit, literally.
  • Currently attempting to install VirtualBox on Keiko’s laptop.
  • Goals this weekend: Find articles, tutorials on QIIME, set up meeting with Lamendella, finish installing VirtualBox and QIIME.
Posted in Andrew, Keiko | Leave a comment

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