Poor per tile sequence quality

[cd1]

We recently performed a couple HiSeq runs, and I'm quite new to NGS analysis.

I'm attaching a representation of the results from FastQC for most of the samples. I'm wondering if anyone knows what might account for the poor sequencing quality.

Thank you!

[Brian Bushnell]

I'm guessing it's poor flow in certain tiles, which yields worse quality with every cycle as the read positions in the colony become increasingly out-of-sync (some percent fail to advance with each cycle).

[cd1]

Thanks Brian! Would the poor flow be due to overloading of sample into the flow cell? Or, are there are reasons for poor flow in specific tiles? (ie: machine-specific reasons or others?)

Thank you!

[Brian Bushnell]

Overloading shouldn't have any impact on flow. Flow problems are typically caused by machine-specific fluidics issues (clogged nozzles, etc), I believe.

[cd1]

Oh, I see. Thanks so much! If anyone else has thoughts on the results, please let me know!

Thank you!