How to install and set up a local UCSC BLAT environment

Downloading BLAT To get BLAT source code: Patching (optional) I decided to make blat a static binary to avoid missing shared library errors. Here’s a patch you can use to modify the blat makefile: You may need static library packages installed on your system. The names of these packages will depend on your version […]

How to get a list of HGNC symbols and names (descriptions)

Here’s a quick method to get HGNC symbols and names that draws upon data from UCSC and the open source project: There’s a Python script in there that I call The pipeline above writes a two-column text file called hgnc_symbols_with_names.txt that contains the HGNC symbol (e.g., AAR2) and its name (e.g., AAR2 splicing factor […]

Speedy BED conversion tool: convert2bed

Finishing touches are in place for my convert2bed tool (GitHub site). This utility converts common genomics data formats (BAM, GFF, GTF, PSL, SAM, VCF, WIG) to lexicographically-sorted UCSC BED format. It offers two benefits over alternatives: It runs about 3-10x as fast as bedtools *ToBed equivalents It converts all input fields in as non-lossy a […]