I'm a bit confused on the meaning of tile, in per tile quality new to NGS revision. Does the tile refer to the actual place where you put a sample or what is this in reference to?
A flow cell in case of Illumina used to be imaged in discrete sections which were referred to as tiles.
Tile based imaging is still used in smaller throughput sequencher models (e.g. MiSeq etc) but for large production sequencers (e.g. NovaSeq) it is my understanding that a continuous movie of the flowcell surface is captured and analyzed in real-time in memory of the attached computer.
From learn.gencore.bio.nyu.edu site:
Samples are loaded into one or more lanes on the flow cell. As @genomax-18713 said, older sequences take static images of discrete sections of each lane for each sequencing cycle. These discrete regions are called tiles. Newer high-scale sequencers take a continuous video of the entirety of the flowcell that is analyzed in real time, so the tile-based images are not used and that terminology is moot.
Per-tile sequence quality is usually used to determine if there are QC issues with either the sample or the lane loading.
Edit: The end of my above statement is incorrect, tiles are still relevant for newer sequencers despite the change in imaging methodology. See the comment from GenoMax below for more info.
Hi, so the tile numbers recorded in read names in NovaSeq reads would just correspond to some fixed locations on the lane, but aren't actually meaningful in any way? Are the read coordinates relative to the tile, or to the lane, the surface, or the whole flowcell?..
NovaSeq reads would just correspond to some fixed locations on the lane, but aren't actually meaningful in any way?
Those numbers are unique identifiers and do have a meaning. See page 72 in this document for details on lanes, swath, tiles.
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