Skewness in RNA-Seq insert size

1

Entering edit mode

9.4 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.

Thanks in advance

skewness insert-size rna-seq rsnorm • 2.2k views

ADD COMMENT • link updated 2.2 years ago by Ram 43k • written 9.4 years ago by ashwini ▴ 100

0

Entering edit mode

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.

ADD REPLY • link updated 2.2 years ago by Ram 43k • written 9.4 years ago by Devon Ryan 104k

0

Entering edit mode

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

ADD REPLY • link updated 2.2 years ago by Ram 43k • written 9.4 years ago by ashwini ▴ 100

Login before adding your answer.