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This final bias is corrected by normalizing the corrected read depths for each usable restriction fragment by the corrected read depths from a euploid reference dataset.
Consider a multiple alignment of the original read, the corrected read and the corresponding genomic region.
Peaks are called where the corrected read density exceeds the threshold.
A final copy number estimate (CNV) estimate was made by calculating the weighted average of the corrected read depths.
The corrected read density threshold is when the calculated probability drops below a pre-determined level (default— P < 0.001).
As a consequence, the size of the corrected read is closely correlated to the sequencing errors of the input long read.
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Read lengths of the corrected reads must be longer than the longest repeat, and have sufficient depth as to cover and resolve the repeat regions.
We provide two utilities for trimming and splitting the corrected reads.
Celera assembler (v. 7.0) [ 14] was used to assemble the corrected reads.
Briefly, mapped reads from the Novoalign output file are corrected for the presence of insertions, deletions or substitutions, then the corrected reads overlapping each genomic feature counted.
As input, it requires the mapping of the original reads and of the corrected reads to the genome in SAM format.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com