title: RNA-Seq of Mycobacterium tuberculosis H37Rv: WT parent grown at pH 6.6
design: Between 0.5-1g of total RNA at 50-100 ng/l were submitted for sequencing. Sample libraries were prepared for RNA-seq using the Ribo-Zero Magnetic Bacterial kit (Epicentre) in connection with TruSeq Stranded Total RNA kit (Illumina).  10-20x106 50bp paired-end reads were obtained for each sample replicate on an Illumina HiSeq 2500. Post-run demultiplexing and adapter removal were performed and fastq files were inspected using fastqc (Andrews S., 2010). Trimmed fastq files were then aligned to the reference genome (M. tuberculosis H37Rv, NC_000962.3) using bwa mem (Li H. and Durbin R., 2009).  Bam files were sorted and merged using samtools (Li H., Handsaker B., et al, 2009 and gene counts were obtained using featureCounts from the Bioconductor Rsubread package (Liao Y, Smyth GK and Shi W, 2014).