tools for calculating nucleotide composition of a gene
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5 months ago
xiaoleiusc ▴ 70

Hi, All,

I wonder if there is any tool to do nucleotide composition analysis to generate figures such as this (link here)? It would be great if the sliding window size could be customized.

Thanks,

Xiao

NGS • 347 views
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5 months ago
bernatgel ★ 3.2k

You should be able to compute the actual nucleotide composition with Biostrings and compute the rolling mean with zoo::rollmean. To plot these values you can use karyoploteR. This example at the karyoploteR tutorial does not do a rolling mean but computed the mean over fixed tiling, but it can help you get started.

Example of a nucleotide frequency plot generated by karyoploteR

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