File Format Converter
perl script to convert between a number of genomic interval file formats: bed, gff, gff3, gtf, tagalign. Allows customized output formatting string to convert any known input format to any output format. Also change chromosome fields as appropriate for different downstream applications. Open the file in a text editor for instructions.

Downsample
perl script to randomly reduce the number of reads in a file. Open the file in a text editor for instructions.

Overlap
perl script to calculate the intersection of two bed files. The resulting file preserves the score of each of the original intervals. Open the file in a text editor for instructions.