Illumina CASAVA runParameters.xml

Question

[rasool.aysha]

Hello,

In the runParameters.xml script of CASAVA 1.8, line 5 of the setup <PairEndFC>false</PairEndFC> is confusing to me since I am entering the identity of my V3 or V4 flowcell later on. I need to know why this is script asking for flowcell in the beginning and in line 14 where: <Flowcell>HiSeq Flow Cell v3</Flowcell>

Answer 1

[Dan D]

You do realize that XML is not a scripting language, but markup language, correct? In other words, it contains information only, no logic.

I can't attest to why Illumina structured their XML like they did, but I'm sure there's a good reason. My best guess is that the separate boolean node prevents the application using the XML data from having to infer whether or not a flowcell is paired-end from its name.

runParameters.xml is automatically created by the HiSeq Control Software which runs on the instrument, and its contents are populated based on user input at the time a sequencing run is initiated.