metagene: paired-end bam as input
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anton.kratz ▴ 60
@antonkratz-8836
Last seen 3 months ago
United States, San Diego, UCSD

Regarding the metagene package (http://www.bioconductor.org/packages/release/bioc/html/metagene.html).

I am using paired-end bam files as input. The plots which I generate with metagene look reasonable, but I am wondering what exactly is plotted. Does metagene consider the first base of each mate, or the middle of the insert?

Basically I am wondering which base(s) are used for producing the plot when using paired-end bam files, and whether one pair leads to one or two "counts" contributing to the underlying matrix.

metagene • 748 views
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@charles-joly-beauparlant-4777
Last seen 4.0 years ago
Canada

Hello Anton,

metagene does not support paired-end reads at the moment. If you use the design to group two paired bam files, it will treat them as replicates.

Charles.

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