Skewness in RNA-Seq insert size
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8.1 years ago
ashwini ▴ 100

Hi,

I aligned Illumina fastq reads (2x100bp) to transcriptome using Bowtie2 and found that the mean insert size is ~180bp and SD ~60bp. By plotting the insert sizes I found that the data is right skewed and the skewness is ~1.69 which was obtained using "skewness" from the package "e1071".

I tried to obtain this type of data from rsnorm where we can specify skewness parameter.

rsnorm(3000000, mean = 180, sd = 60, xi = 1.69)


xi is the skewness parameter.

But the plot I get is more symmetrical and also skewness is 0.69 while the mean and SD remain the same (180bp and 60bp respectively).

I tried with different values for Xi and I always end up with values -1 to 1. So I am confused here.

It will be helpful to know where I am going wrong.

skewness insert-size rna-seq rsnorm • 1.9k views
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Hello ashwini!

It appears that your post has been cross-posted to another site: SEQanswers.

This is typically not recommended as it runs the risk of annoying people in both communities.

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I am sorry! I thought I will get answer from either of them.