Categories: "Encode" or "Job Notes"

ENCODE cell lines

February 24th, 2010
These are some of the cell lines that are used in the various analysis of the ENCODE project. The first two are so-called tier-1 lines and covered by all the different types of experiments within ENCODE, the others are tier-2 lines, additionally there… 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 »

Proserver Setup

November 2nd, 2009
Installing and Running Proserver to serve data via DAS The Distributed Annotation System (DAS) is an elegant way of sharing data and using data from diverse sources. More information at http://www.biodas.org and on these blog pages. The Proserver is a… more »

Assessing Gene Predictions

November 2nd, 2009
Calculating prediction rate TP = true posisitives (correctly identified) FP = false positives (overpredicions) TN = true negatives (correctly un-called) FN = false negatives (missed) Specificity = TP / (TP + FP) Sensitivity = TP / (TP + FN)… more »