Changes between Initial Version and Version 1 of BIOS_RnaSeq

Timestamp:

Sep 19, 2016 5:02:19 PM (8 years ago)

Author:

jamverlouw

Comment:

--

BIOS_RnaSeq

@@ +1 @@
+= RNASeq protocols=
+
+In a nutshell, all raw RNAseq datasets on Grid will look like the following:
+
+* sample AD1NNNACXX-1-2
+ * srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/RNASeq/AD1NNNACXX-1-2/AD1NNNACXX-1-2_R1.fg.gz
+ * srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/RNASeq/AD1NNNACXX-1-2/AD1NNNACXX-1-2_R2.fg.gz
+
+* sample AD1NNNACXX-1-4
+ * srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/RNASeq/AD1NNNACXX-1-4/AD1NNNACXX-1-4_R1.fg.gz
+ * srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/RNASeq/AD1NNNACXX-1-4/AD1NNNACXX-1-4_R2.fg.gz
+
+The locations of sample information, file location, md5sum, etc are stored in the [wiki:BIOS_Metadatabase Metadatabase].
+
+== SRM location ==
+All RNA sample datasets are stored at srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/RNASeq/. 
+
+Note: all data are also copied to the Grid archive and where they are backuped.
+
+== Directory naming ==
+Each sample is to be uploaded into its own, separate directory. The directory name is formatted as follows:
+{{{
+<flowcell ID>-<lane ID>-<index ID>/
+}}}
+For instance:
+{{{
+AD1NNNACXX-1-2/
+}}}
+
+== File naming ==
+Files should follow the same naming scheme as the directories: 
+
+=== GZipped .fastq's ===
+Fastq files, required for alignment, are to be formatted as follows:
+{{{
+<flowcell ID>-<lane ID>-<index ID>_R1.fq.gz
+<flowcell ID>-<lane ID>-<index ID>_R2.fq.gz
+}}}