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Przemol / seqplots

:chart_with_upwards_trend:SeqPlots - An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps.
http://przemol.github.io/seqplots
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Asking for advise: how to normalize different samples before plotting? #31

Closed ktrns closed 6 years ago

ktrns commented 7 years ago

seqplots_2datasets_1geneset

Hi,

I am using seqplots to generate aggregate plots. However, different samples are sequenced to different depths. For example, sample1 contains 4x as many reads as sample2. However, in the plot it seems as if it was 2x as many reads. If I normalize the samples by RPM, sample1 even appears to have a lower signal than sample2, even though they are replicates and should overlap. Do you have any comments or ideas on how to normalize sequencing data before subjecting them to seqplots?

Many thanks in advance, Katrin

Przemol commented 6 years ago

For CHIP-seq experiments I recommend rBEADS: https://github.com/Przemol/rbeads