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Old 10-28-2008, 10:09 AM   #1
cgregg
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Default How to make great wiggle plots and Seq figures

Hi,

Does anyone have suggestions for software that easily generate great publication quality figures to display custom tracks - specifically wiggle plots of RNASeq data? The UCSC browser custom tracks are OK, but fuzzy if you try to build figures and IGV from the Broad seems better, but lacks a nice display of splice variants and a clear Y axis.

Thanks for any help.

Chris
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Old 10-28-2008, 03:34 PM   #2
ECO
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I really like nimblegen's SignalMap for graphic representation. It can't open HUGE gff/bed files, but the default settings make some nice graphs.
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Old 10-28-2008, 03:40 PM   #3
cgregg
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Thank you. I will give that a try!

Chris
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Old 10-29-2008, 07:35 AM   #4
mgogol
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UCSC isn't fuzzy if you use the PDF/PS link to export postscript. You can edit postscript files with something like Adobe Illustrator to make pretty nice figures.

You could also make your own figures using R, either with your own code or using something like the GenomeGraphs package.
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Old 10-29-2008, 08:15 AM   #5
cgregg
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Thanks, I will try that. I didn't know about that feature.

Chris
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Old 08-09-2012, 12:41 AM   #6
oxydeepu
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Hi all,

I have question on how to plot wiggle tracks. I just have a wig file and a reference genome fasta. Can anyone suggest me some ways i can plot the wiggle into a nice figure.

Thanks in advance
Deepak
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