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Summary

The third file is prefix.lima.summary, shows how many ZMWs have been filtered, how ZMWs many are same/different, and how many reads have been filtered.

ZMWs input                (A) : 213120
ZMWs above all thresholds (B) : 176356 (83%)
ZMWs below any threshold  (C) : 36764 (17%)

ZMW marginals for (C):
Below min length              : 26 (0%)
Below min score               : 0 (0%)
Below min end score           : 5138 (13%)
Below min passes              : 0 (0%)
Below min score lead          : 11656 (32%)
Below min ref span            : 3124 (8%)
Without SMRTbell adapter      : 25094 (68%)
With bad adapter              : 10349 (28%) <- Only with --bad-adapter-ratio
Undesired hybrids             : xxx (xx%) <- Only with --peek-guess
Undesired same pairs          : xxx (xx%) <- Only with --different
Undesired diff pairs          : xxx (xx%) <- Only with --same
Undesired 5p--5p pairs        : xxx (xx%) <- Only with --isoseq
Undesired 3p--3p pairs        : xxx (xx%) <- Only with --isoseq
Undesired single side         : xxx (xx%) <- Only with --isoseq
Undesired no hit              : xxx (xx%) <- Only with --isoseq

ZMWs for (B):
With same pair                : 162244 (92%)
With different pair           : 14112 (8%)
Coefficient of correlation    : 32.79%

ZMWs for (A):
Allow diff pair               : 157264 (74%)
Allow same pair               : 188026 (88%)
Bad adapter yield loss        : 10112 (5%) <- Only with --bad-adapter-ratio
Bad adapter impurity          : 10348 (5%) <- Only without --bad-adapter-ratio

Reads for (B):
Above length                  : 1278461 (100%)
Below length                  : 2787 (0%)

Explanation of each block:

  1. Number of ZMWs that went into lima, how many ZMWs have been passed into the output file, and how many did not qualify.
  2. For those ZMWs that did not qualify, the marginal counts of each filter; each filter is explained in great detail elsewhere in this document.
  3. For those ZMWs that passed, how many have been flagged as having a same or different barcode pair. And what is the coefficient of variation for the barcode ZMW yield distribution in percent.
  4. For all input ZMWs, how many allow calling a same or different barcode pair. This a simplified version of, how many ZMWs have at least one full pass to allow a different barcode pair call and how many ZMWs have at least half an adapter, allowing a same barcode pair call.
  5. For those ZMWs that qualified, list the number of reads that are above and below the provided --min-length threshold (details see here).

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