These tools are created for analyzing the peaks or read distributions (bedgraph, wiggle format) derived from next-generation sequencing such as ChIP-seq or RNA-seq.

The included tools are:

• ga_overlap: checks the overlapping and return the overlapping, non-overlapping, and original file with ov/nonov flags.
• ga_reads_summit: calculates the average read distribution around summit or specific position such as TSS (Transcription Start Site).
• ga_reads_summit_all: calculates read distributions around ALL summits or specific positions such as TSS (Transcription Start Site).
• ga_calc_dist: calculates the distance between two peak sets or inter-summit distance.
• ga_reads_region: calculates read amounts in the specific regions such as peak, up-stream regions.
• ga_nuc_region: calcultes nucleotide content in the specified regions.
• ga_nuc_summit: calcultes nucleotide content distributions around summits.
• ga_deltaG: makes the wiggle file of the free energy difference between the duplex and single-strand states from fasta file.
• ga_RPKM: calculates the expression levels as RPKM.
• ga_reads_gene: calculates read distributions around genes (not supported yet...).
• ga_flanking: picks up the regions (genes) which flank peaks/summits (not supported yet...).

• GCC compiler
• GNU C Library(glibc)
• zlib
• (optional) R