Category: "Job Notes"

QSEQ File Format

January 6th, 2011
Each record is one line with tab separator in the following format: - Machine name: unique identifier of the sequencer. - Run number: unique number to identify the run on the sequencer. - Lane number: positive integer (currently 1-8). - Tile number:… more »

GENCODE: Generating release files

January 4th, 2011
A. input sources -ensembl core database with gene models, stable ids and xrefs -vega database of same release for id-lookup -3way pseudogene file with gene ids: from Yale, based on pre-dump file from same release -selenocystein file: mysql -… more »

Ensembl Core Database Schema Diagram

November 26th, 2010
To understand the concept of Ensembl and learn how to query the tables I find it extremely useful to have a schema diagram of the database in front of me. This can be generated by using the schema.sql and foreign_keys.sql files from the sql directory… more »

AnnoTrack: Data maintanance

December 8th, 2009
Regular updates The following Perl scripts update the data and re-set priorities and flags. They usually update Havana annotation data, but all other sources can be checked as well by activating the entry in the config file. They run as cron-job every night, but can also be run manually if needed. The cron-job is executed from svn/gencode/tracking_system/perl/scripts/cron_jobs.pl. Common parameters are: more »

Conditional Formatting in Ms Excel

November 12th, 2009
To change the format of a cell based on the content of that or another cell conditional formatting can be used. For simple things and up to three options the dialog "Format"-"Conditional Formatting" can be called after selecting the target cell. You can… more »