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Table 1 Table of the times and the RAM memory peaks reached during the RNA-Seq analysis for the eight pipelines

From: ARPIR: automatic RNA-Seq pipelines with interactive report

  Alignment Quantification DEA Time (h) RAM (Gb)
1° pipeline TopHat2 Cufflinks cummeRbund 35 3.3
2° pipeline Hisat2 StringTie Ballgown 4 4.3
3° pipeline Hisat2 featureCounts DESeq2 4 4.3
4° pipeline Hisat2 featureCounts edgeR 4 4.3
5° pipeline STAR Cufflinks cummeRbund 5 30
6° pipeline STAR featureCounts DESeq2 4 30
7° pipeline STAR featureCounts edgeR 4 30
8° pipeline Kallisto Kallisto Sleuth 2 2.2
  1. The longest pipeline was found to be TopHat2-Cufflinks-cummeRbund, while the shorter kallisto-sleuth. The RAM memory peaks are maintained in all cases except for STAR pipelines below 5 Gb