ggbio, overview circular plot, BSgenome, bam to GRanges?
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pterry • 0
@pterry-6902
Last seen 20 months ago
United States

Hello,

I would like to display and compare two files, one a BSgenome file, the second contains aligned reads in a bam file. I would like to display these on a 'circular overview plot' to compare them (see chpt 4 of the ggbio vignette, 'ggbio: visualization toolkits for genomic data', Oct. 13, 2014).

The examples in section 4.1.2 are using as input, data in GRanges format. So to display my two files, must I convert each to GRanges format? If so, how to do it?

Thanks,
Philip Terry
Univ. Nebraska-Lincoln

 

ggbio GRanges ggbio GRanges • 1.4k views
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Can you specify what you mean with comparing a BSgenome object with a BAM file? The first contains a reference sequence, while the second represents a set of reads. Do you want to show the reference sequence as one layer/track and a pileup of the reads as a second layer?

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