I recently got very bad sequencing results from a Miseq Illumina run. The average Sequence qualities declined very early, leading to low read lengths after quality clipping.
When I looked at the respective FastQC-results i noticed a very strange pattern in the "Quality per tile"-Plot (see attached .png file):
I get less than average quality for cycles 80-280 almost exclusively at tiles 1112-1119 and then again at tiles 2115-2119.
What I find extremely strange is the apparent "smear" of bad quality from tiles 1112-1119, which then seems to stop abruptly. I do not quite understand what is up with tiles 1120-2100: Are they simply not shown in this plot, or should I assume that Tiles 1119 and 2101 are neighbors?
usually when I see examples of bad quality-per-tile patterns, bad quality tiles seem to be more distributed along the flow cell and have consistently bad quality during all cycles (e.g. this example).
In my case, however i seem to have a double smear-pattern of temporarily bad quality tiles, broadly around cycle 175.
Does anybody have experience in interpreting such plots?
I would like to understand what the tile-designations "1101"-"2119" mean, exactly.
Could something like bubbles have formed themselves at cycle ~80 and then just burst sometime around cycle 280?
In that case, how can it be that this pattern seems to occur twice on the flow cell around roughly the same time? Pure coincidence?
When I looked at the respective FastQC-results i noticed a very strange pattern in the "Quality per tile"-Plot (see attached .png file):
I get less than average quality for cycles 80-280 almost exclusively at tiles 1112-1119 and then again at tiles 2115-2119.
What I find extremely strange is the apparent "smear" of bad quality from tiles 1112-1119, which then seems to stop abruptly. I do not quite understand what is up with tiles 1120-2100: Are they simply not shown in this plot, or should I assume that Tiles 1119 and 2101 are neighbors?
usually when I see examples of bad quality-per-tile patterns, bad quality tiles seem to be more distributed along the flow cell and have consistently bad quality during all cycles (e.g. this example).
In my case, however i seem to have a double smear-pattern of temporarily bad quality tiles, broadly around cycle 175.
Does anybody have experience in interpreting such plots?
I would like to understand what the tile-designations "1101"-"2119" mean, exactly.
Could something like bubbles have formed themselves at cycle ~80 and then just burst sometime around cycle 280?
In that case, how can it be that this pattern seems to occur twice on the flow cell around roughly the same time? Pure coincidence?
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