Table 1.
Input files for the RNA-seq analysis pipeline
| A) Factors | B) Contrasts | C) Classes | ||||
|---|---|---|---|---|---|---|
| Experiment | Strain | Time | A_F71Y-WT | BSU00490 | green | CodY |
| WT1 | WT | T1 | B_R61K-WT | BSU01650 | green | CodY |
| WT2 | WT | T1 | C_R61H-WT | BSU01660 | green | CodY |
| F71Y1 | A_F71Y | T1 | Null-WT | BSU01670 | green | CodY |
| F71Y2 | A_F71Y | T1 | BSU01680 | green | CodY | |
| R61K1 | B_R61K | T2 | etc… | … | … | |
| R61K2 | B_R61K | T2 | BSU03981 | red | CcpA | |
| R61H1 | C_R61K | T2 | BSU03982 | red | CcpA | |
| R61H2 | C_R61K | T2 | BSU03990 | red | CcpA | |
| null1 | Null | T2 | BSU04160 | red | CcpA | |
| null2 | Null | T2 | BSU04470 | red | CcpA | |
| etc… | … | … | ||||
A) File describing the experiments and containing information of experiment replicates, B) File with the comparisons (contrasts) to be made, C) File with groups of genes/RNAs of interest