Output Files
primetime generates several output files during its execution. All the plots for QC are stored in the primetime_QC folder. Then the main result of primetime containing the activity and fold-change values is stored in the primetime_results folder, together with some additional plots.
Bellow we list all the QC and results files with a brief description.
1. Quality Check outputs
Inside the primetime_QC folder, several QC plots will be placed.
| File Name | Description |
|---|---|
barcode_correlations.pdf | Correlation of Log2(cDNA/pDNA) for different barcodes of each replicate. |
replicate_correlations.pdf | Correlation of Log2(cDNA/pDNA) — after averaging the different barcodes — for each sample. |
bleedthrough_estimation.pdf | Estimation of the amount of pDNA bleedthrough (percentage of cDNA counts coming from pDNA) for each replicate. |
distribution_of_BC_counts.pdf | Distribution of the counts from all the barcodes of each replicate. |
expected_vs_observed_pDNA_counts.pdf | Correlation of your pDNA counts (observed) with the ones of our lab (expected). |
read_counts.pdf | Total amount of reads coming from each replicate. |
2. Main Results
| File Name | Description |
|---|---|
primetime_results.txt | Main result file containing adjusted p-values, fold-change values for each TF, and TF activity for each condition. |
primetime_volcano.pdf | Volcano plot of the differential activity results. |
primetime_lollipop.pdf | Lollipop plot showing the activity of each TF for both conditions, highlighting the differentially active ones. |
Click here to read a deeper description on the expecter outcomes of primetime.
Additional files
primetime also saves some additional files in the tmp_primetime folder, such as the barcode counts, and the results of the barcode clustering.
These files provide a comprehensive overview of the TF activity analysis and can be used for further downstream analysis.