On Wed, Aug 15, 2012 at 11:13 AM, Du, Jianguang <jia...@iupui.edu> wrote:

>  Dear All,
> I am analyzing the downloaded RNA-seq datasets. However I am not sure how
> much is Mean Inner Distance between Mate Pairs for these paired-end
> datasets.
> Take a paired-end RNA-seq dataset as an example, there is a description
> for this dataset in SRA database of NCBI: "Layout: PAIRED*, Orientation: *
> 5'-3'-3'-5'*, Nominal length: *400*, Nominal Std Dev: *20"
 At first I thought the Mean Inner Distance between Mate Pairs should be
> 325bps because the length of reads on both ends is 36bps. However
> when I aligned the sequence of the paired reads on to transcripts and
> genome using BLASTn, the distance between the paired reads is about 200bps.
> How should I decide the Mean Inner Distance between Mate Pairs in my case?

The information from SRA is likely only an approximation.  SRA does not
validate these details, I do not think.

You can probably use the distribution from your data as the best estimate.


> Jianguang Du
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