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We use a Bioanalyzer to calculate average fragment size as recommended by Illumina.
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I recommend you generate an insert-size histogram computationally, as well, to help determine whether this is a problem with chemistry, or with short inserts. You can do so without a reference with BBMerge, like this:
bbmerge.sh in=reads.fq ihist=ihist_merging.txt reads=1000000
...or if you do have an assembly, via mapping like this:
bbmap.sh in=reads.fq ref=reference.fa nodisk ihist=ihist_mapping.txt reads=1000000
The two approaches have different biases, and both will give somewhat different answers than Bioanalyzer.Comment
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