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 | ||||||