Pipeline description and methods

This page holds the general description and methodology for the alignment and gene quantification pipeline. Also on this page are links to the pages specifically dedicated to the settings and output of the different runs. See the attachment for a graphical representation of the pipeline.

Full run implementation list

Read more at the pipeline todos page.

Git repository

For an overview of outstanding issues and submitting tickets please use the pipeline's Gitlab repository hosted at the LUMC.

​https://git.lumc.nl/rp3/RNA-seq-pipeline/issues

Pipeline output and history

The current output and history of our pipeline are described at dedicated run specific pages. Find the latest one in the table below for the most recent run output and specifics.

Run page	Start date	Sample count	Database	Output location	Data on SRM	In RunDB
5ddcae7*	2013-10-04	2270+30+30	​rp3_rna_run_20131004	RP3/production/5ddcae7/	Y	Y
7ea6b13	2013-11-25	115	​rp3_rna_run_20131004	RP3/production/7ea6b13/	N	N
6d401ed*	2014-01-23	64	​rp3_rna_run_20131004	RP3/production/6d401ed	Y	Y
v1.0.4	2014-02-24	6	​rp3_rna_run_20131004	RP3/production/v1.0.4	Y	N
v2.1.0	2014-06-10	-	​rp3_analysis	RP3/production/v2.1.0	Y	Y
v2.1.3 complete freeze1 run to process all BIOS samples	2015-07-10	Remaining ~2000 in BIOS project	​rp3_analysis	RP3/production/v2.1.3	Y	Y

*In rundatabase the metrics of these runs are joined and stored under v0.0.0 as this is one run.

General Methodology

Read more at Methodology

Replication Test

Read more at Replication test