Platform Unit For Sam Read Group

Question

[Johan]

I'm wondering exactly what the "Platform unit" means in the read group header in the SAM format. This is what I found in the specification:

Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD). Unique identier.

Since I have Illumina data, does this mean that I should use something like this: "FC706VJ.1" - assuming that the flowcell barcode is "FC706VJ" and the lane is 1. (The example names are from the FASTQ enty at wikipedia)? And If this is the case, does any one know if it is possible to extract the flowcell name from the report.xml generated Casava? I have a hunch that this is the same as the RunFolder attribute - but I might be wrong.

Answer 1

[Johan]

Ok. I will answer my own question with what I have figured out this far. The flowcell-barcode is a unique identifier (as described in the documentation quoted above) of the flowcell. In the report.xml file it should be included as an attribute called "FlowCellId" in the MetaData tag. However, this does not always seem to be included. This is then coupled with the lane(s) that the sample was run on to form the platform unit.