Download FUN-LDA scores

The precomputed FUN-LDA scores can be downloaded at here.

Help document

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.

Usage:

The output columns are:

Options:


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.