Track files

For each sequencing library, for each annotation family, ncPRO-seq generates two compressed track files in http://genome.ucsc.edu/goldenPath/help/bedgraph.html BedGraph format to describe read mapping in sense and antisense direction of annotation items respectively.

As we have listed in 3.1, there is an option called GENOME_TRACK_OPTIONS which allow users to select different subsets of reads mapped in the genome to generate BedGraph formatted track files.

In BedGraph formatted track files, only reads which has the same genome cooridates are grouped and the total number of grouped reads are considered as the height of the peak in the track. Overlapped but not identical reads are considered as different hits, rather than combine them as a single hit.

All track files outputed from ncPRO-seq can be directly uploaded to http://genome.ucsc.edu/index.html UCSC browser / other genome browser for visualization. Note that multipy layers of color inside peaks in the track indicates the presence of overlapped hits.