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• 13:10, 29 May 2026 Haars0011 talk contribs deleted page RNA-seq analysis (content was: " === Typical commands used for analyzing RNA-seq with Tophat (including Bowtie2 as aligner).=== * Examples are RNA-seq (stranded) from pig aligned against the pig reference genome (''S. scrofa'' - 10.2) * Tophat, Bowtie2, Picard and GATK need to be in PATH or loaded as modules (e.g.: module load SHARED/bowtie/2-2.2.1; module load SHARED/tophat/2.0.11) * Bowtie2 index (made with bowtie2_build) of reference genome (need only to be made ones) * PCR duplicates removed with Picar...")