The precomputed FUN-LDA scores can be downloaded at here.
To extract FUN-LDA scores the bigWigAverageOverBed utility is required. It can be downloaded from the Genome Browser website at http://hgdownload.cse.ucsc.edu/admin/exe/.
Here is the current help page for this utility:
bigWigAverageOverBed v2 - Compute average score of big wig over each bed, which may have introns.
The output columns are:
To use the utility, you must prepare a bed file, a tab-separated 4-column file. The first column is the chromosome, the second is the zero-based coordinate of the position of interest, the third is that zero-based coordinate plus one, and the fourth is a unique identifier for the position.
Here is an example of the contents of a bed file, example.bed:
A bed file can have arbitrarily many rows.
Then bigWigAverageOverBed can be used as follows, assuming E059.valley9.c89.bigwig and example.bed are in the working directory:
It produces a 6-column file, example.tab, looking like this:
The last column, average over the covered bases, is the score for this position. The first column includes the unique id. The -bedOut option to bigWigAverageOverBed can be used to include the other columns from the input .bed file in a .bed output file.