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Mycobacterial infection induces a specific human innate immune response

This repo contains the code for the following manuscript:

Blischak, J. D. et al. Mycobacterial infection induces a specific human innate immune response. Sci. Rep. 5, 16882; doi: 10.1038/srep16882 (2015).

Other links related to this publication:

Description

We have collected gene expression data from macrophages isolated from six individuals. They were infected with different strains of Mycobacterium tuberculosis and other bacteria (nine total "conditions" including infections and controls). Furthermore, we collected data at 4, 18, and 48 hours post-infection.

Main analysis files

  • differential-expression.Rmd - Performs DE analysis with limma/voom.

  • joint_analysis.Rmd - Runs Cormotif to classify genes according to their expression patterns across the infections.

  • candidate_genes.Rmd - Plots expression of immune response genes.

  • reQTL.Rmd - Compares FDRs from DE analysis of response eQTL-associated genes (identified in Barreiro, Tailleux et al. 2012) to the background of expressed genes.

Preprocessing steps

Uses R package ngspipeline.

Sort files

./organize_files.R ../data/flow-cells.csv ../samples/

Map reads

find ../samples/ -name "*fastq.gz" -exec bash -c \
'echo "./map_fastq.R {} ~/subread-indexed-genomes/hg19/hg19" | \
qsub -l h_vmem=16g,bigio=1 -V -N map-`basename {}` -cwd -o stdout -e stderr' \;

Count reads per gene

mkdir std-counts
find ../samples/ -name "*bam" -exec bash -c \
'echo "./count_reads.R -sl ../data/gene_lengths.txt {} ../data/exons.txt -o /KG/jdblischak/counts" | \
qsub -l h_vmem=8g -V -N count-`basename {}` -cwd -o std-counts -j y' \;

Combine annotation and gene counts

library(ngspipeline)
anno  <-  "../data/annotation.txt"
count_files <- list.files("/KG/jdblischak/counts/",
                          pattern = "counts$", full.name = TRUE)
out_name <- "../data/counts_per_run.txt"
add_anno_to_counts(anno, count_files, out_name)

Sum gene counts per sample

library(ngspipeline)
sum_counts_per_sample("../data/counts_per_run.txt",
                      "../data/counts_per_sample.txt")

License

The code is available via the GPLv3 license (because we use multiple R/Biocodncutor packages which are GPL'd). The text is available via the CC BY 3.0 license.