It includes a method for effectively increasing the resolution obtained from low-coverage experiments by utilizing breakpoint information from paired end sequencing to do positional refinement.
Typical resequencing experiments involving at least 30-fold coverage will be largely tolerant of low levels of cross contamination but experiments designed to identify rare variants in a population, or low coverage sequencing experiments may be more sensitive.
Low coverage deposition experiments of molecule 2 were also performed at 140 K on both substrates.
However, while MS evidence can be used to verify protein-coding potential, the low coverage of proteomics experiments implies that the reverse is not true.
This is a low coverage RNA sequencing experiment, and so you may have to zoom out a bit in order to see the data.
The reason for the acceptance of only partially overlapped genes is that evidence based methods might only partially predict a gene, e.g. due to low coverage in RNA-Seq experiments.
For example, if we look at the Macro-F1 values only for the best method on each dataset (see Table 6 and Table 7), we can note that the overall prediction performance of the methods is still low - i.e. Macro-F1 values are around 0.9 only for methods with low coverage in the 2-class experiments and only 0.6 for the 3-class experiment.
On the technical side, I mainly criticize the low coverage of the BS-seq experiments, which to my opinion do not provide enough information for the performed analyses; and the RNA-seq experimental setup with essentially no replication.
Our data show that AT-rich regions (>55%), regions with an overall low probe density (<3) and small exons (on average 90 bp) yield a low coverage, which also varies significantly between experiments.
Upon an initial endonucleotic cleavage, MNase displays an exonuclease activity that continues with the degradation of DNA [ 40], leading to digested areas that we identified as low coverage regions (LRs) in our sequencing experiments (see Methods).
