5.3.1 Pausing analysis
The identification of global pause sites was based on reads exceeding three standard deviations above the mean of the surrounding 200 nucleotides L. Stirling Churchman 2011. The Pausing Index (PI) was then calculated as the ratio of read density within the proximal promoter and read density within the gene body, while the Elongation Index (EI) was determined to eliminate the effect of the large 5′ peak commonly associated with paused polymerase. Specifically, EI was defined as the ratio of 5′ read density (first 25% of the gene after the first 500 bp) and the 3′ read density (the remaining 75%).
5.3.2 What it does?
The module scans the entire genome to identify pause sites and calculate the pausing index and elongation index for all genes.
5.3.3 Example
nasap pausing_sites --forward_bw ./tmp/bw/forward.bw --reverse_bw ./tmp/bw/reverse.bw --output_root ./tmp
Parameters
| parameter | description |
|---|---|
| --forward_bw (Required) | Forward bigwig file. |
| --reverse_bw (Required) | Reverse bigwig file. |
| --cores (Optional) | Multiprocess num. |
| --output_root (Optional) | Output root directory. |
5.3.4 Results
Global pausing sites file
| File | Directory |
|---|---|
| global pausing sites | bed/pausing_sites.bed |
Global pausing distribution plot
The pausing sites are distributed in whole genome.
Pausing files
| File | Directory |
|---|---|
| proximal_pause_sites | bed/proximal_pause_sites.bed |
| pausing index | csv/pi.csv |
| elongtaiont index | csv/ei.csv |
Proximal pausing sites to tss distribution
The proximal pausing distribution plot visualizes the distribution of proximal pausing sites across genes or genomic regions.