Computational protocol: CD82 hypomethylation is essential for tuberculosis pathogenesis via regulation of RUNX1-Rab5/22

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Protocol publication

[…] FASTQ files from RNA-seq experiments were clipped and trimmed of adapters, and low-quality reads were removed using Trimmomatic. Quality-controlled FASTQ files were aligned to the UCSC hg19 reference genome using STAR (version 2.5.1) aligner software with three mismatches. To measure differential gene expression, DESeq2 with the default parameters was used. A subset of condition-specific expression was defined as showing a 1.0 log2-fold difference and P-adj < 0.01 in expression between MTB Rv and MTB Ra. RNA-seq experiments were normalized and visualized using HOMER after preparing custom tracks for the UCSC Genome Browser (http://genome.ucsc.edu/). […]

Pipeline specifications

Software tools Trimmomatic, STAR, DESeq2, HOMER
Databases UCSC Genome Browser
Application RNA-seq analysis
Diseases Neoplasms, Tuberculosis