Bioinformatics Exercise 1-Integrated use software-2

Using humann2:

=================== reference Chen Yu greatly study document ==========================

HUMAnN2 is a description of microbial metabolic pathways. Use the sequence information of a macro genome or a macro transcription group.

Http://huttenhower.sph.harvard.edu/humann2

The order of installation is: Bowtie2 ===> Metaphlan2 ===> HUMAnN2

(Personal recommended installationAnaconda, which integrates multiplepythonpackages, you don't have to worry about missing anything when installing other software.NumPy,scipythese additionalpythonit's wrapped.. )

install nothing to say, download the installation package (source), unzip, set the environment variable on it. It's important to note thatHUMAnN2relies on two databases (Chocophlanand theUniref), his installation package contains only these two databases.DEMO version. So we'll first download the full version. Use Thunderbolt, simple rough (smiling face)

Chocophlan : http ://huttenhower.sph.harvard.edu/humann2_data/chocophlan/full_chocophlan_plus_viral.v0.1.1.tar.gz

Uniref : http://huttenhower.sph.harvard.edu/humann2_data/uniprot/uniref_ec_filtered/uniref90_ec_filtered_1_1. tar.gz

Configuration:

I use Thunder to download the file has a problem, after decompression is empty = = so use the command to download:

Humann2_databases--download Chocophlan Full/home/pxy7896/downloads/humann2/humann2/data/chocophlan_full4

The command automatically configures the path to the database, so it is ready to be placed.

ids= "G45084 G45072 G45071 G45109 G45125 G45124 G45049 G45054 G45121 G45099"

For S in ${ids}

Do

Humann2--input ${s}_pe_1.fastq.gz--OUTPUT/HOME/PXY7896/DESKTOP/20161205/RESULT2

Humann2--input ${s}_pe_2.fastq.gz--OUTPUT/HOME/PXY7896/DESKTOP/20161205/RESULT2

Done

Ran a night and produced a lot of files ...

Bioinformatics Exercise 1-Integrated use software-2