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track scaling
16-Aug-2013, 04:58 PM
Post: #1
track scaling
I noticed that tracks from different studies sometimes have substantial differences in the number of footprints indicated on y axises. The tracks seem to be normalized to the maximum density in the particular study. This makes it convenient in terms of comparing density within one transcript, but not between studies when the goal is to see the differences in gene expression between different conditions. Is there a way to rescale the tracks relative to the maximum density in the display?

primus inter pares Angel
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19-Aug-2013, 10:23 AM
Post: #2
RE: track scaling
Gwips-viz uses an auto scaling approach where track is rescaled to the local maximum, (the highest peak displayed in the track), the reads aren't normalised. To change the track view to a set range click on link to the study of interest. Change autoscale option in "Data view scaling" to "use vertical view setting". You may also want to change the vertical viewing range also.

You should bear in mind however that the number of alignments is dependent on the sequencing depth of the study. Different studies (and different tracks within studies) can have large differences in the total number of reads mapped.
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