GBS Data Management
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Revision as of 12:19, 23 August 2018 by Mlucas (Talk | contribs) (Created page with "GBS Sequence Data Management consists of the following tasks: # Download of GBS sequence data files from sequencing facilities. # Verify the integrity of downloaded GBS files...")
GBS Sequence Data Management consists of the following tasks:
- Download of GBS sequence data files from sequencing facilities.
- Verify the integrity of downloaded GBS files.
- Create or rename GBS sequence files to conform to the standard GBS file naming format.
- Filtering of GBS sequence file to remove short reads of less than 75bp (Nextseq files only).
- Update wheatgenetics gbs table flowcell, lane, num_lines and md5sum columns for each file.
- Checking % valid reads in each GBS file and % reads in associated with each blank well.
- Checking DNA quantification values for blank wells relative to other wells.
- Storage of GBS files on Beocat in /bulk/jpoland/sequence GBS sequence file repository
- Backup of GBS files to external NAS.
The exact method for executing these tasks is dependent on the sequencing facility that produced the data.