Qiime Basic Tutorial

Qiime Basics


Table of contents


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What is qiime?

QIIME (canonically pronounced chime) stands for Quantitative Insights Into Microbial Ecology.It is a command line tool.


Why do we use it

How do we use it?

We type commands in the command prompt, specify input files and get output files
installation: virtualbox
results : tsv files, html files

OTU picking

Command line basics


Command
Example
Description
1.     ls
ls
ls -alF C:/myfolder/
Lists files in current directory
List in long format
2.     cd
cd tempdir
cd ..
cd ~dhyatt/web-docs
Change directory to tempdir
Move back one directory
Move into dhyatt’s web-docs directory
3.     mkdir
mkdir graphics
Make a directory called graphics
4.     rmdir
rmdir emptydir
Remove directory (must be empty)
5.     cp
cp file1 web-docs
cp file1 file1.txt
Copy file into directory
Make backup of file1
6.     rm
rm file1.txt
rm *.tmp
Remove or delete file
Remove all file
7.     mv
mv old.txt new.txt
Move or rename files
8.     more
more log.txt
Look at file, one page at a time
9.     lpr
lpr log.txt
Send file to printer
10.   -h
validate_mapping_file.py -h
Online manual (help) about command
https://www.tjhsst.edu/~dhyatt/superap/unixcmd.html

Installation


Important Points

Validate mapping file : http://qiime.org/scripts/validate_mapping_file.html

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