Glitches
Glitches are controlled by three parameters, given as a comma-delimited list of numbers:
- rate: how often glitches occur
- size: how much random sequence is added at a glitch site
- skip: how much read sequence is lost at a glitch site
This page illustrates read glitches using dotplots. The dotplots compare:
- x axis: a 10 kbp sequence in Badread before glitches are added
- y axis: the sequence after glitches (but before sequencing errors)
| 5000,100,100 | 1000,100,100 | 200,100,100 |
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The three dotplots above show 10 kbp reads where the glitch rate is varied. You can see that the smaller the value, the smaller the space between glitches.
| 1000,100,0 | 1000,0,100 | 1000,100,100 |
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These dotplots show the effect of the size and skip parameters. The first has a size of 100 and a skip of 0. This means that each glitch adds random sequence but loses no real sequence, resulting in a longer glitched sequence. The second is the opposite, a size of 0 and a skip of 100, making the glitched sequence shorter than the original. The third has size and skip both equal to 100, so the glitched sequence should on average be the same length as the original.
The examples shown above are particularly glitchy to illustrate the concept. Badread's default value is 10000,25,25 for a modest amount of glitches. Or you can use 0,0,0 to turn glitches off entirely:
| 10000,25,25 | 0,0,0 |
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