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Table 1 DE-kupl parameters and resources used for analyzing epithelial–mesenchymal transition data (12 libraries) using the t-test or DESeq2 method (GENCODE masking)

From: DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition

Parameter/resources Value
nb_threads 8
min_recurrence 6
min_recurrence_abundance 5
pvalue_threshold 0.05
lib_type Stranded
  t-test DESeq2
Maximum memory usage 54 GB 53 GB
Maximum disk used (1) 7 GB 42 GB
Running time (1) 4 h 2 m 6 h 33 m
  1. (1) excluding reference genome and transcriptome indexing for the annotation step