Global metrics about a run

[ClemBuntu]

Hello everyone,

I have to collect some metrics about a MiSeq run.
I used CASAVA for demultiplexing (namely the configureBclToFastq.pl script). I obtained a folder wich contains some XML files, where there are some tables with few metrics like number of Cluster, numbler of cluster PF, and % intensity after 20 cycles. By the way, why 20 ? Why not 15 or 40 ? I think these page are generated by IVC but I'm not sure about that.

Looking for other metrics on the web, I found this page : https://sites.google.com/a/brown.edu...110_ad1v25acxx which really looks like to the one I have. My question is how to get the same kind of table ? (with density and error rate etc.)

Thanks !

[GenoMax]

Sounds like you have access to the original flowcell folder. You can use illumina sequence analysis viewer (windows only) to look at various data metrics associated with the run: http://support.illumina.com/sequenci...iewer_sav.html

In the CASAVA analyzed folder you want to look at the "Demultiplex_Stats.htm" file that is found in the flowcell_ID/Unaligned/Basecalls_*/ folder.

[ClemBuntu]

Unfortunately, I work on a unix computer cluster so I can't use your tool...

Indeed I do have acces to the original flowcell folder. I had a look to the "Demultiplex_Stats.htm" file, but it doesn't contain the density or the error rated for example, unlike to the link of my previous message. But maybe can I calcul the density by myself using the number of tiles ? I'm thinking about something like that : sum (nb cluster) / nb Tiles * tiles size but where can I find the tile's size ? Is it the same for all Illumina's sequencer ?

[GenoMax]

There are two other threads the describe other ways of accessing the run metrics information from unix.

http://seqanswers.com/forums/showthread.php?t=27342

http://seqanswers.com/forums/showthread.php?t=22474

Example you had linked may have been analyzed (one can do alignments etc on the machine itself) on the MiSeq and thus has additional information.

[ClemBuntu]

Yes you're right, I've just learned the biologist has this kind of data because they're given by the machine itself as you said... Well thank you !