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This step removed the regions with low reads (no methylated CGs present in our sequencing library).
We found that those with extremely low reads failed to be consistently detected using PCR.
If the read quality is low, reads can be trimmed e.g. with the freely available software tool trimmomatic [ 32].
Transcripts with low reads counts were excluded by only keeping transcripts with at least 50 reads in at least two libraries.
We removed peaks with low reads per million (<1 RPM in all samples) or high-input signal (>0.5 RPM); or peaks that were blacklisted by the ENCODE consortium analysis of artifactual signals in mouse or human cells (Kundaje, 2013).
A base mean threshold of ten was set to eliminate contigs with few counts, since contigs with very low reads typically have inaccurate expression patterns due to sampling error.
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The majority of missed true positives had low read coverage.
To assess performance at low read depths (≤15×), 10 S.
Previous studies associated low read count with false positive expression profiles [ 93, 94].
However, the estimation of BAF is unreliable in regions of low read depth [ 14].
The chances of low read coverage to some regions of the sequence are very high.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com