I am involved in an RNAseq project in which mutliple tissues of an organism are being analysed. Normally the company doing the analysis runs between two and five lanes of each biological replicate and, after examining the appearance of the BigWig files on the UCSC browser I choose two to merge and work up through the Tuxedo pipeline and one to display on a customized UCSC browser view of tracks. Especially for BigWig, this results in comparable tracks of a managable size.
A recent tissue sample was only run on a single lane, but the fast.qz files I received were 5-10x larger than normal, as were the resulting Bam and BigWig files. Is there a program that would allow me to take a representative 'sample' from these files (e.g. one fifth) to avoid having to load a very large file on the UCSC browser?