Downloading BLAT To get BLAT source code: Patching (optional) I decided to make blat a static binary to avoid missing xyz.so 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 […]
Category Archives: commandline
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 MyGene.info project: There’s a Python script in there that I call get_hgnc_names_for_symbols.py: 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 […]
Replacing multiple spaces with one tab in BSD (OS X) sed
Press Ctrl-V and the Tab character where you see [TAB]: