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Data and analysis releated to the Pediatric Longitudinal Study of Elemental Diet and Stool Microbiome Composition study
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1_Data
2_Code
3_Result
4_Doc
5_Analysis
6_Shiny/PLEASE_Shiny
README.md

README.md

PLEASE data analysis by Eric Z Chen

This is a repo for my paper (Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease. Cell Host & Microbe. 2015). This repo includes the preprocessed data used in this paper.

We called the data used in this paper as PLEASE data, which are shotgun metagenomic sequencing data. For details, please refer to my paper.

Data

Raw fastq files

All the fastq files are saved in the folder 1_COMBO_PLEASE on the server. This folder contains four sub-folders:

  • 1_Raw_Fastq: the raw fastq files.
  • 2_Quality_Filter: the fastq files after removing the low quality reads.
  • 3_Remove_Human_DNA: the fastq files after removing the low quality reads and human reads.

Clinical data and sample information

  • The raw clinical data are in the folder 1_Data/Raw_Data/Clinical_Information/.
  • The processed clinical data and sample information are in the folder 1_Data/Processed_Data/Sample_Information/.

Bacterial abundance by MetaPhlAn

The MetaPhlAn outputs for COMBO samples and PLEASE samples are in the following folders. The "unclassfied" taxa were removed and the total relative abundance in each sample were normalized to be one. "P","F","G","S" at the beginning of each file indicate taxonomic levels "phylum", "family", "genus", "species".

  • 1_Data/Raw_Data/MetaPhlAn/COMBO
  • 1_Data/Raw_Data/MetaPhlAn/PLEASE

Phylogenetic trees by PhyloPhlAn

I used the Phylogenetic trees by PhyloPhlAn to calculate the phylogenetic diversity. However, the trees from PhyloPhlAn can not be directly used (it caused some errors) and I processed the tree files. "P","F","G","S" indicate taxonomic levels "phylum", "family", "genus", "species".

  • 1_Data/Raw_Data/Phlogenetic_tree

Analysis

Fastq data processing

  • The raw fastq data were processed by FASTX to remove low quality reads.
  • Then the processed reads were aligned to human genome to remove human reads by Deconseq. The code is in 1_COMBO_PLEASE/Code_for_Human_Reads_Removal.

Bacterial abundance quantification by MetaPhlAn

  • The processed reads were used as input for MetaPhlAn. Since MetaPhlAn can only take single end reads as input and our data are pair-end reads, the paired reads (R1 and R2) were provided as two single end reads to MetaPhlAn. I also tested MetaPhlAn on the first read pair (R1) only and the results are quite similar to the previous ones.

Reference

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease. Cell Host & Microbe 2015

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