Tuesday, 2 August 2011

Nick Loman blogs PGM 316 1st Impressions

 While eagerly waiting for our own PGM to be installed for 316 chip support, I came across Nick's review on their own 316 run. Which has pretty impressive output! 

"Our first two runs of 316 chips yielded an impressive 251Mb and 209Mb respectively! Mean read length was about 110bp."

Other interesting factoids for the impatient 

we've loaded the chips way higher than we are used to with the 314 – densities of 76-82%

This reflects a change to the protocol – when we were running 314 chips we were told to load fewer beads to get better coverage – and from our trials when we loaded at 41, 43 and 46% density on the 314 chip the 41% run did do best. The 314 chip has about 1.2m wells, so we were filling about 550k wells. About two-thirds of those wells were live spheres (meaning they have DNA on them) and out of those about two-thirds pass the quality filter – about 200k reads in all (~20Mb data).

The 316 chip has 6.3m wells and we're filling about 5m of these. A little under half are passing the quality filters, meaning we're getting about 2.25m reads.


Do hop on over to the original post to see FASTQC plots of the reads

Ion Torrent 316 First Impressions

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