Human polymerase usage sequencing (Pu-seq) R-scripts & demo data v1.0

Initial setting

- Rcpp package has to be installed in advance to R environment.
- The R working directory have to be set to the directory which contain 'README.md'(./).
- './sub' and './rcpp' contains R and rcpp source codes which are required to be implemented with script above. For this reason, the directory structure within 'script' has to be maintained.
- wigToBigWig have to be executable (located in $PATH)

Provided R-script

./script/bincount-csv_to_pol-usage-wig.R

- Generating polymerase usage data in the wig format from genome-wide bin count data, which is produced by Perl script: pe-sam-to-bincount.pl (available at the GitHub site: https://github.com/yasukasu/sam-to-bincount).
- In the default setting, files in ./data/count.csv will be inputted and outputted files will appear in the working directory.

./script/pol-usage-wig_to_ini-index-wig.R

- Generating initiation index data in the wig format from polymerase usage data.
- Inputting files (.wig or .bw) are required to be written in the code. In the default setting, polymerase usage data in ./data/wig will be inputted and outputted files will appear in the working directory.

./script/pol-usage-wig_to_fork-index-wig.R

- Generating fork index data in the wig format from polymerase usage data.
- Inputting files (.wig or .bw) are required to be written in the code. In the default setting, polymerase usage data in ./data/wig will be inputted and outputted files will appear in the working directory.

./script/pol-usage-wig_to_coupling-index-wig.R

- Generating coupling index data in the wig format from polymerase usage data.
- Inputting files (.wig or .bw) are required to be written in the code. In the default setting, polymerase usage data in ./data/wig will be inputted and outputted files will appear in the working directory.

./script/bincount-csv_to_pol-usage-wig.R

- Generating coupling index data in the wig format from genome-wide bin count data.
- In the default setting, files in ./data/count.csv will be inputted and outputted files will appear in the working directory.

Provided wig format datasets

Genome-wide bin counts datasets

./data/count.csv/pol-e-m630f.f-w1000.count.csv
./data/count.csv/pol-e-m630f.r-w1000.count.csv
./data/count.csv/pol-e-plus.f-w1000.count.csv
./data/count.csv/pol-e-plus.r-w1000.count.csv
./data/count.csv/pol-a-y865f.rep1.f-w1000.count.csv
./data/count.csv/pol-a-y865f.rep1.r-w1000.count.csv
./data/count.csv/pol-a-plus.f-w1000.count.csv
./data/count.csv/pol-a-plus.r-w1000.count.csv

Polymerase usage data

./data/wig/pol-e-m630f_pol-usage_watson_w1000_MA30.bw
./data/wig/pol-e-m630f_pol-usage_crick_w1000_MA30.bw
./data/wig/pol-a-y865f_pol-usage_watson_w1000_MA30.bw
./data/wig/pol-a-y865f_pol-usage_crick_w1000_MA30.bw

Initiation index

./data/wig/ini-index.pol-e-a.w1000.MA30-15.rep1.wig

Fork index

./data/wig/Pol-e-a.fork-index.leftward.norm_z.w1000.MA30-15.bw
./data/wig/Pol-e-a.fork-index.rightward.norm_z.w1000.MA30-15.bw

Coupling index

./data/wig/Pol-e-a.coupling-index.rightward.w1000.MA30.bw
./data/wig/Pol-e-a.coupling-index.leftward.w1000.MA30.bw

Replication fork directionality (RFD)

./data/wig/RFD.pol-e-a.w1000.MA30.wig