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?
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