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