genome informaticssoftware

Create BigWig files with DeepTools

To display data as bar graphs along the genome e.g. in the UCSC genome browser, you can create BigWig files. The underlying Wig format is described in more detail here.
BigWig is the binary version (described here), that allows compressing the data and streaming of the data from a remote location to the machine running the display (i.e. the genome browser) on demand.

To create and work with the data various software options are available, my current recommendation is:

DeepTools, a “suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data”. The docu pages show more options, but to get started install with:

conda install -c bioconda deeptools

or

pip install --user deepTools

and create a BigWig from a Bam file:

bamCoverage -b Seqdata.bam -o Seqdata.bigWig

Originally a Galaxy workflow, DeepTools2 can run on the command line or as an API. It was published by Fidel Ramírez et al.

You can display the data in the UCSC browser by adding a custom track (more details) in the form on the track control page using a line like the following to point to your file that needs to be internet-accessible:

track type=bigWig name="My Big Wig" description="Seqdata BigWig file" bigDataUrl=https://your.server.com/Seqdata.bigWig