Skip to content

a-solovyev12/bioc3301_project

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

6 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

BIOC3301 project

This repository contains scripts (PBS and Python) and part of the data analysis for the UCL BIOC3301 project.

Read the project report here.

pbs_scripts

Scripts that were submitted to the Cirrus HPC via the portable batch system. Contains the basic QIIME pipeline (OTU assigning, filtering, and demultiplexing) as well as scripts used for further analysis (e.g. beta-diversity or construction of OTU table for specific taxonomy level). This foler does not contain scripts used on a local machine, however, the full list of available scripts can be found at http://qiime.org/scripts/index.html.

metadata

This foler stores tsv files that contain external data both for our project and the Earth Microbiome Project (EMP). They include physicochemical properties of the soil, location, temperature, etc. Note that the EMP dataset was filtered to contain only soil samples (i.e. the marine sediments, etc. were excluded).

jupyter_scripts

ipynb scripts for analysis and manipulation of our and EMP data.

beta_div

This folder contains data required to construct the phylogenetic tree (representative sequences were picked and aligned) and the tree file itself. The Phylo.io resouce is convenient for tree visualisation.

Other folders

correlations contains txt files which are output of various correlation analyses applied to our project and EMP data.

figures stores images (graphs, phylogenetic tree), some of which were used in the report.

taxa_summary stores OTU tables for specific taxonomy levels (L1-L6) rarefied at a depth of 600 reads.

About

part of final year UCL Biochem project

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published