= Updating to Reggie 4.33 =

== A. Before updating Reggie ==

=== 1. New pipeline script ===

The `readlength_averager.awk` script is a new script that must be installed (see #1335). Install the script at a suitable location and make sure to update reggie-config.xml with the new path.

=== 2. Create a new Tophat software alignment item ===

A new software item for the Tophat alignment is needed since the --mate-inner-dist parameter is calculated base on `ReadLengthAvgR1` and `ReadLengthAvgR2` annotations instead of `ReadString`. The new software items should be included as a project default and the old software item should be removed and SCAN-B access should be changed to Read-only (used to be Read-Use).