Chunk #121 — Materials and methods — Read alignment for the Bottomly et al. and Pickrell et al. datasets

Source

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.

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Reads were aligned using the TopHat2 aligner [65], and assigned to genes using the summarizeOverlaps function of the GenomicRanges package [60]. The sequence read archive fastq files of the Pickrell et al. [17] dataset (accession number [SRA:SRP001540]) were aligned to the Homo sapiens reference sequence GRCh37 downloaded in March 2013 from Illumina iGenomes. Reads were counted in the genes defined by the Ensembl GTF file, release 70, contained in the Illumina iGenome. The sequence read archive fastq files of the Bottomly et al. [16] dataset (accession number [SRA:SRP004777]) were aligned to the Mus musculus reference sequence NCBIM37 downloaded in March 2013 from Illumina iGenomes. Reads were counted in the genes defined by the Ensembl GTF file, release 66, contained in the Illumina iGenome.