I have been looking at a library run in Hiseq using fastQC. Usually I get good Per tile sequence quality, with the entire area looking bluish (OK quality throughout). But this time I get tiles that appear to give consistently low quality reads over the entire read sequence. The thing is - I thought this was due to a problem in the flow cells, but I see the same cells appearing to have bad reads over several different runs. The strangest bit - the same experiment was run on two different occasions; it was too large to sequence in one illumina run so they divided it into two groups. Group no.1 looks bad (the same flow cells give low quality reads at the exact same places) but group 2 - the libraries from the same experiment look bad while the quality of the rest of the libraries look great...
I checked other runs - some looked great, others had the same problem... so whatever it is it's not consistently happening at every run.
I found a webpage describing this - please look at the second figure from the top, I see something like that, just worse: https://sequencing.qcfail.com/articles/position-specific-failures-of-flowcells/
Anyone knows what this means?