= 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
}}}