Dear All, Can anyone recommend on what do to with Illumina lib that is supposed to be MP, but looks more like PE? This problem should be "minor" according to http://grcf.jhmi.edu/hts/protocols/MatePair_2-5kbSamplePrep_1005363_RevB.pdf (page 7, "Inward and Outward Facing Paired Reads"), but this minor problem turns out to be a major one out here... I guess i should just turn off "-GENERAL:use_template_information" at all for this library, right? I am attaching a plot of insert size distribution to show what the problem is about. Sincerely, Nestor
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Mate-Pair lib.png
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