Getting a gene list fom eCLIP bigBED file

Question

[o.hickman]

I'm using eCLIP .bigbed files downloaded from the ENCODE project. I'm try to get a gene list - which genes have tags.

I've been trying to use the "Operate on genomic intervals - Join" function in Galaxy. This I've used before for .bed files. But it doesn't seem to work on .bigbed files.

Converting them to .bed files appears to be non-trivial as well.

Any help getting this to work, or an alternative method for getting a gene list for these data would be most appreciated!!!

Thanks in advance.

Answer 1

[Alex Reynolds]

I don't know what the format of an eCLIP file is, but you can convert BigBed to BED with the bigBedToBed tool in the Kent toolkit.

If you're on OS X, you can install them via Homebrew:

$ brew install homebrew/science/kent-tools

For other platforms, you can install binaries (including bigBedToBed) one by one via http://hgdownload.cse.ucsc.edu/admin/exe/

Once you have this tool (or toolkit) installed, you run:

$ bigBedToBed input.bb output.bed

Once you have the BED file, you can do set operations via the BEDOPS kit with bedops, bedmap, etc., e.g.:

$ bedmap --echo --echo-map-id-uniq eCLIP.bed genes.bed > gene_IDs_overlapping_eCLIP_regions.bed

[o.hickman]

Hi Thanks Alex, Thanks for your answer. I'm using windows. What platform do you suggest I use to install these tools? Oliver

[Alex Reynolds]

Run a version of Linux within VirtualBox. https://en.m.wikipedia.org/wiki/VirtualBox