Question: How To Decide "Mean Inner Distance Between Mate Pairs"?
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Du, Jianguang • 380 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?
Thanks.
Jianguang Du
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modified 6.3 years ago
by
Sean Davis • 220
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written
6.3 years ago by
Du, Jianguang • 380
