help with colour and smoothingWindow

[STIRPARO Giuliano Giuseppe RIC]

Hi, I have some data like this:

 

file_reverse.BedGraph

 

track type=bedGraph smoothingWindow=16

1 3201074       3201125 -0.06

1 3201215       3201266 -0.06

1 3201839       3201844 -0.06

1 3201845       3201891 -0.06

1 3201947       3201998 -0.06

1 3210947       3210998 -0.06

1 3211290       3211341 -0.06

1 3216209       3216260 -0.13

1 3216369       3216420 -0.13

1 3254766       3254817 -0.06

 

file_Forward.bedGraph

 

track type=bedGraph smoothingWindow=16

1 3152649       3152700 0.06

1 3152983       3153030 0.06

1 3153031       3153035 0.06

1 3215255       3215306 0.06

1 3215307       3215358 0.06

1 4243564       4243575 0.06

1 4243575       4243615 0.13

1 4243615       4243626 0.06

1 4496431       4496482 0.06

 

I have two question.

1) I would like to merge the data and obtain a uniq file and represent the strand coverage with different color.

2) I would like to smooth my data (I have already try with smoothingWindow=16 but the file look the same as smoothingWindow=off)

 

Thanks for ideas or suggestions.

 

Best

 

Giuliano

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[Luvina Guruvadoo]

Hello Giuliano,

Thank you for your question. To have wiggle data on forward and reverse strand, you need two separate tracks with separate data sets. There is no information in wiggle data about strand. The two data sets can be included in a single composite track in a track hub with forward in one color, and reverse strand data in a separate color. The Y-axis can be inverted for one and thereby placing the two tracks back-to-back so they appear to be a single track, forward strand data up, and reverse strand data down.

The 'smoothing window' only works on the pixel display window, it does not work on the actual data itself. For data points that fall together in the display in smoothing window size pixels, the data points will be merged together in a running average. At different levels of viewing, this changes the observed data view. When the data points are separated by more than the smoothing window size pixels, the actual data values will be graphed as they are. It is only when the data view begins to merge together inside one smoothing window pixel size, they begin to combine into a smoothed average.

Also see this previously answered question:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/tHaAxlck7AY/BjEyfULc0xwJ

I hope this helps. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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