Q2: orientation and position

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Lu Xie

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Apr 10, 2011, 5:14:53 PM4/10/11

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The last row, Pos, is the position on coding strand, right?
The bases are on the reverse strand, right?
So when we draw the graph, we shall go from left to right, but with
the bases on coding strand, right?

Marcel Schulz

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Apr 10, 2011, 7:50:02 PM4/10/11

to computational-ge...@googlegroups.com, Lu Xie

Hi Lu,

On Sun, Apr 10, 2011 at 5:14 PM, Lu Xie <fir...@gmail.com> wrote:

The last row, Pos, is the position on coding strand, right?

yes.

The bases are on the reverse strand, right?

No the bases shown are from the forward strand.

So when we draw the graph, we shall go from left to right, but with
the bases on coding strand, right?

As the transcript is on the reverse strand the arrows should point from right to left otherwise everything stays the same as the example from the lecture. You should take the bases from the forward strand.