From: Modeling and cleaning RNA-seq data significantly improve detection of differentially expressed genes
Cleaning method | #genes after cleaning | #DEGs total* | #DEGs with | |||
---|---|---|---|---|---|---|
Any annotated function | Regulation of biological process | Transcription regulation | Molecular function regulator | |||
RNAdeNoise | 25,356 | 2439 | 2144 | 338 | 92 | 40 |
Raw data | 37,336 | 2392 | 2086 | 326 | 87 | 38 |
HTSFilter | 22,907 | 2348 | 2056 | 319 | 83 | 38 |
counts > 3 | 26,089 | 2309 | 2025 | 320 | 84 | 38 |
counts > 5 | 25,215 | 2287 | 2005 | 318 | 85 | 36 |
counts > 10 | 23,973 | 2128 | 1898 | 310 | 85 | 38 |
FPKM > 0.3 | 23,237 | 1930 | 1770 | 304 | 87 | 34 |
½samples > 3 | 24,173 | 2363 | 2063 | 360 | 84 | 38 |