5. Toolkit

bam_to_coverage.sh

It requires bedtools to count a coverage at each position.

bam_to_fiveprime.sh

Regacy script to count a read truncation at each position.

bed_to_pars_format.py

Convert bed to tab (used in Section. 2)

read_collapse.py

To overcome bowtie2 error.

read_truncate.py

To overcom bowtie2 error.

prober_add.py

Convert PROBer output to PARS tab format

tab_to_csv.py

Convert PARS tab format into csv