Computational protocol: Genome-scale DNA methylome and transcriptome profiling of human neutrophils

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Protocol publication

[…] RNA was sequenced on the Illumina HiSeq 2000 sequencer (Illumina, USA) with a single-ended, 51-bp run producing raw fastq files. The quality of the RNA-Seq data was assessed using FASTQC program as described previously,. The RNA-seq reads were mapped to the human genome (assembly GRCh37) using TopHat (v2.0.11) (see Code availability 5), transcripts were assembled, abundances (Fragments Per Kilo base per Million or FPKM) of transcript were estimated. In our primary paper, for analysis of differential expression we used with Cufflinks (v2.2.0) package with default parameters. For exon usage analysis, Human gene models were flattened and reads assigned to exon bins and counted using HTSeq (v0.5.4p5). Differential exon usage was calculated using the DEXseq (v1.8.0) package. […]

Pipeline specifications

Software tools FastQC, TopHat, Cufflinks, HTSeq, DEXSeq
Application RNA-seq analysis
Organisms Homo sapiens