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Normalized display of RNA-seq data

asked 2013-04-30 00:43:47 -0600

Irina Voineagu gravatar image

I found GenomeBrowseto be a very good alternative to IGV for RNA-seq data. I only had two issueswhile looking at BAM files: (1) Is it possible to adjust the display parameters so that each coverage peak is normalized to the total number of reads in the BAM file? This would be very useful for visually comparing expression across samples. (2) Is it possible to export the plots as jpeg/pdf?

thank you!

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answered 2013-04-30 21:06:46 -0600

Hey Irina,

I'm glad you have found GenomeBrowse useful!

There is no normalization of the coverage data per say, but notice that the Y axis auto-scales to the extents of your data. So two samples side-by-side will show a similar profile of exon coverage even if one has 10x as much data.

If you want the Y-axis to be set to the same scale, you can select multiple plots and edit the Y axis limits in the plot's control panel.

On your second question, we have plans for a more extensive "save image" feature, but for now we suggest taking a screenshot and cropping it to your relevant plots.

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Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.


Asked: 2013-04-30 00:43:47 -0600

Seen: 444 times

Last updated: Apr 30 '13