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This process yields reads that are about 12% longer.
However, there are many short reads that are not aligned to any known gene models.
Short reads that are not present in known exons might represent any kind of splicing events.
Such dropped out reads combined with reads that are placed in self-contained clusters are referred to as "singletons".
The oriented RNA-seq protocol produces reads that are oriented according to the RNA molecules they originate from.
Figure 4A shows reads that are mapped using TopHat [ 35].
Reads that are compatible with an isoform are the reads that are possibly generated from the isoform.
Precision is the fraction of mapped reads that are correctly mapped and recall is the fraction of correctly mapped reads that are retrieved.
In Stage #1, all reads that are not covered by a gene model were filtered out.
Contigs are stretches of assembled reads that are free of branching conflicts.
This results in a larger number of reads that are misaligned.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com