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high-frequency peaks?

Posted: Tue Feb 26, 2013 3:33 am
by cjones
Does anyone know what's up with these strange reads? I can't recall seeing this before: the peaks are small and compressed horizontally:

Re: high-frequency peaks?

Posted: Tue Feb 26, 2013 4:40 pm
by wleung
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 4666 times