high-frequency peaks?

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cjones
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Joined: Sun Feb 04, 2007 10:19 pm
Location: Moravian College, Bethlehem PA
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high-frequency peaks?

Post by cjones » Tue Feb 26, 2013 3:33 am

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
HiFreqPeaks.png (71.06 KiB) Viewed 3496 times
Chris Jones
Assoc. Prof. of Biology
Moravian College
Bethlehem PA

wleung
Posts: 185
Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

Re: high-frequency peaks?

Post by wleung » Tue Feb 26, 2013 4:40 pm

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):
change_trace_horizontal_scale.png
Different trace horizontal scales
change_trace_horizontal_scale.png (185.39 KiB) Viewed 3492 times

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