high-frequency peaks?
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cjones
- Posts: 99
- Joined: Sun Feb 04, 2007 10:19 pm
- Location: Moravian College, Bethlehem PA
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high-frequency peaks?
Does anyone know what's up with these strange reads? I can't recall seeing this before: the peaks are small and compressed horizontally:
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- HiFreqPeaks.png (71.06 KiB) Viewed 3496 times
Chris Jones
Assoc. Prof. of Biology
Moravian College
Bethlehem PA
Assoc. Prof. of Biology
Moravian College
Bethlehem PA
Re: high-frequency peaks?
The "high frequency" peaks is an artifact of the "Display traces for all reads" function in Consed.
The "Display traces for all reads" function tries to scale all the reads to the same horizontal scale. Consequently, in the case where there are deleted bases in some of the reads (i.e. danafos7163.g1, 22421411F13.b1) compared to the other reads and the consensus, the reads with the extra bases would appear much closer together in the "Display traces for all reads" window.
You can reproduce this issue by changing the horizontal scale for a single trace (e.g. 07528075K19.b1):
The "Display traces for all reads" function tries to scale all the reads to the same horizontal scale. Consequently, in the case where there are deleted bases in some of the reads (i.e. danafos7163.g1, 22421411F13.b1) compared to the other reads and the consensus, the reads with the extra bases would appear much closer together in the "Display traces for all reads" window.
You can reproduce this issue by changing the horizontal scale for a single trace (e.g. 07528075K19.b1):
- Different trace horizontal scales
- change_trace_horizontal_scale.png (185.39 KiB) Viewed 3492 times