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 | |