I am aware that the fragment size depends on the strength of sonication. The insert size is the length of actual genomic sequence without adapter.
My confusion is: What are the considerations when deciding the fragment size? Say, we have an target region to be sequenced. What is difference of making the fragment size of 200 and making the fragment size of 400?
Besides, assuming we apply paired end sequencing and our read length is 150bp, the insert size of 400 makes an inner size of 100 and the insert size of 200 makes the paired end reads overlapping each other by 50bp (I guess we don't want the insert size < read length, right?). How would this two options makes difference? Is there a preference or consideration on whether making the paired end reads overlapping to each other? Really appreciate any comments :)