Changes between Initial Version and Version 1 of BIOS_Pipeline


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Timestamp:
Sep 19, 2016 4:54:24 PM (8 years ago)
Author:
jamverlouw
Comment:

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  • BIOS_Pipeline

    v1 v1  
     1= Pipeline description and methods =
     2
     3This 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.
     4
     5== Full run implementation list ==
     6
     7Read more at the [wiki:BIOS_Pipeline/pipeline_todo pipeline todos] page.
     8
     9== Git repository ==
     10
     11For an overview of outstanding issues and submitting tickets please use the pipeline's Gitlab repository hosted at the LUMC.
     12
     13https://git.lumc.nl/rp3/RNA-seq-pipeline/issues
     14
     15== Pipeline output and history ==
     16
     17The 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.
     18
     19||= Run page =||= Start date =||= Sample count =||= Database =||= Output location =||= Data on SRM =||= In RunDB =||
     20||[wiki:BIOS_Pipeline/5ddcae7 5ddcae7*]||2013-10-04||2270+30+30||[https://metadatabase.bbmrirp3-lumc.vm.surfsara.nl:6984/_utils/database.html?rp3_rna_run_20131004 rp3_rna_run_20131004]||RP3/production/5ddcae7/|| Y || Y ||
     21||[wiki:BIOS_Pipeline/7ea6b13 7ea6b13]||2013-11-25||115||[https://metadatabase.bbmrirp3-lumc.vm.surfsara.nl:6984/_utils/database.html?rp3_rna_run_20131004 rp3_rna_run_20131004]||RP3/production/7ea6b13/|| N || N ||
     22||[wiki:BIOS_Pipeline/6d401ed 6d401ed*]||2014-01-23||64||[https://metadatabase.bbmrirp3-lumc.vm.surfsara.nl:6984/_utils/database.html?rp3_rna_run_20131004 rp3_rna_run_20131004]||RP3/production/6d401ed|| Y || Y ||
     23||[wiki:BIOS_Pipeline/v1.0.4 v1.0.4]||2014-02-24||6||[https://metadatabase.bbmrirp3-lumc.vm.surfsara.nl:6984/_utils/database.html?rp3_rna_run_20131004 rp3_rna_run_20131004]||RP3/production/v1.0.4|| Y || N ||
     24||[wiki:BIOS_Pipeline/v2.1.0 v2.1.0]||2014-06-10||-||[https://metadatabase.bbmrirp3-lumc.vm.surfsara.nl:6984/_utils/database.html?rp3_analysis rp3_analysis]||RP3/production/v2.1.0|| Y || Y ||
     25||v2.1.3 complete freeze1 run to process all BIOS samples||2015-07-10||Remaining ~2000 in BIOS project||[https://metadatabase.bbmrirp3-lumc.vm.surfsara.nl:6984/_utils/database.html?rp3_analysis rp3_analysis]||RP3/production/v2.1.3|| Y || Y ||
     26
     27{{{
     28#!div style="font-size: 90%"
     29*In rundatabase the metrics of these runs are joined and stored under v0.0.0 as this is one run.
     30}}}
     31
     32== General Methodology ==
     33
     34Read more at [wiki:BIOS_Pipeline/Methodology Methodology]
     35== Replication Test ==
     36
     37Read more at [wiki:BIOS_Pipeline/ReplicationTest Replication test]
     38