Preseq lc_extrap fails when with extremely low read depth, and produces the following error message:
ERROR: too many defects in the approximation, consider running in defect mode.
From a maintainer of preseq:
Preseq uses the observed duplicate count histogram to extrapolate
the expected number of new distinct reads will be gained with additional
sequencing. This will not work if the duplicate count histogram is not
sufficiently full, which may be happening in the 2.5M read samples.
Runnning preseq in defect mode (specified by the -D) solves the problem. Alexei has tested the changes (using the -D flag) by running preseq lc_extrap with good and bad data. With good data resulting NRF values are unchanged, and with bad data preseq does not error out.
Preseq
lc_extrapApproximation ErrorPreseq
lc_extrapfails when with extremely low read depth, and produces the following error message:ERROR: too many defects in the approximation, consider running in defect mode.From a maintainer of preseq:
Runnning preseq in defect mode (specified by the
-D) solves the problem. Alexei has tested the changes (using the-Dflag) by running preseqlc_extrapwith good and bad data. With good data resulting NRF values are unchanged, and with bad data preseq does not error out.