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The choice of 200 bp was because the insert sizes of the data we analyzed were mostly between 150 and 200; we also used 100 bp as a threshold and similar patterns of results were observed (data not shown).
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Unfortunately, we did not obtained the complete sequence, because the insert size of clone P3DP22F02 was only 578 base pairs.
Because the insert size usually exceeds the length of a single read, read-pairs may match up unique regions surrounding repeats that are longer than the read length.
The insert sizes range from 25too 143 kb, with an average size of 82 kb.
The insert sizes were 1030-bp (III) and 650-bp (IV), separately.
The insert sizes of both libraries were close to expectations.
The insert sizes ranged from 0.5 to 3 kb, with an average insert size of 1.5 kb.
This is because the concentration of DNA in the plugs would significantly affect the methods and results of size selection on agarose gels, thus the insert sizes of the BIBAC clones resulted from the DNA [ 38].
The validity at 10 kb of these scaffolds is low because SOPRA's estimate of the insert size is not accurate.
Consider M read-pair libraries, which are sorted in the order of increasing insert sizes and the associated decision rules Extend i(P) for 1 ≤ i ≤ M. We process the libraries in this order because our analysis revealed that the smaller is the insert size of a library (and its variation), the more reliable is the decision rule for this individual library.
Gaps can occur in the fragmented BAC assemblies since the insert size of the pair end reads is 500 bp.
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