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Table 2 DE-kupl pipeline results for the epithelial–mesenchymal transition experiment

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

Files Description Number of k-mers Sizes
   or contigs
raw_counts (no filter) Matrix of k-mers counts 707,067,278 (not generated)
  from all libraries
filtered_counts.tsv.gz Matrix of all k-mer counts from 92,525,450 1.9 GB
  all libraries with recurrence filters
masked-counts.tsv.gz Matrix of counts after 40,398,848 728 MB
  GENCODE masking
   t-test DESeq2 t-test DESeq2
diff-counts.tsv.gz Counts with differential 3,813,418 6,102,447 186 MB 510 MB
  expression test, filtered on  
  adujsted P value  
merged-diff-counts.tsv.gz Differentially expressed k-mers 133,690 169,613 3.0 MB 18 MB
  assembled into contigs  
  1. This is a description of output files sequentially generated by DE-kupl. The numbers of k-mers and contigs correspond to the number of lines in each file