Plus and minus strands plotted together
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4.3 years ago
firatuyulur ▴ 310

Hi all, I am working on a GRO-Seq data and I want to plot a graph like one these figures, plus and minus strands are reversely merged on the same line. I know that UCSC genome browser can handle this, but in many ways, it becomes user-UNfriendly. So does anyone know a tool or GUI which can plot a graph like this?

GRO-Seq ChIP-Seq Figure • 2.0k views
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Entering edit mode
4.3 years ago
firatuyulur ▴ 310

For the ones who have suffered from the same problem; Apparently, GRO-Seq figure is independent of the tool. It is possible to get a visualization as in the link above with any browser. I used Homer for GRO-Seq analysis. The trick is, when it comes to generating the bedgraph using makeUCSCfile command, first separate +/- strands using makeUCSCfile tagDirectory/ -strand + -o plus_strand.bedGraph and for - strand, makeUCSCfile tagDirectory/ -strand - -neg -o minus_strand.bedGraph. the command with -neg will give you a bedGraph with (-) values. before merging them, you may need to remove the trackline information since it may cause an error when sorted. then with using a simple cat command, merge the two, then sort them using sort -k1,1 -k2,2n fileName.bedGraph. then gzip your bedGraph. Now you can even put it to IGV and it will give +/- strands in the same line.

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