What should I do to ensure that the reads produced are of correct length?

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  1. Read truncation can incur when sequencing reads from fragments that are shorter than the parameter READ_LENGTH. With reasonable settings it should only affect a spurious part of the reads when using heuristic filter settings, i.e., the Metropolis-Hastings MCMC algorithm used with parameter SIZE_SAMPLING= MH.

    To completely avoid it ensure that Filtering is on, that the SIZE_DISTRIBUTION is not permissive for any fragments shorter than the read length, and that SIZE_SAMPLING is set to an exact filter (i.e., RJ or AC).