Question: How To Decide "Mean Inner Distance Between Mate Pairs"?
6.3 years ago by
Du, Jianguang • 380
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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