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A rarefaction analysis was performed to estimate the coverage of the microbial community in both sequencing datasets; as expected, sequencing data from the GS FLX Titanium platform provides a far more complete view of the underlying community, while the GS FLX sequencing run was not carried out to saturation.
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As expected, additional sequencing data from each NGS platform improved the assembly statistics (Table 2).
Given the reduction in sequencing cost, it is expected that sequencing data will be predominantly paired-end.
Sequences obtained were BLAST analyzed and matched to the expected sequences, confirming that the correct templates had been amplified (data not shown).
All designed primers (Table 2) amplified cDNA with a single band at the expected size and of the expected sequence, based on the cassava database sequences from which the primers were designed (data not shown).
The S. aureus and P. aeruginosa PNA probes did not cross react with any of the organisms tested, whereas the E. coli PNA probe, as expected from sequence data, also detected Shigella species.
As expected, tag sequence data from different biological samples were properly discriminated by the 4-bp index sequences.
It was expected that sequence data would be very accurate as all QTL genotypes were included in the data and LD was no longer limiting the accuracy of the prediction.
One would expect that deep sequencing data should provide a more accurate measurements of the VAF for each mutation due to the higher read counts.
These are fairly low polymorphism rates that would be expected if comparing human sequencing data to the human reference genome.
Comparing the levels of expression around the peaks of 20E in N5 and N6, these approximately patterns correspond to what would be expected based on the sequencing data.
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