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English students will have to cite material they have read to support the positions they take.
We therefore agree that, despite our wish to minimize parameters and avoid arbitrary cutoffs, requiring at least one (uniquely aligned, high quality) RNA read to support editing is reasonable.
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"I always have something going for pure pleasure and I always have something that I am reading to support something that I am working on".
We found the WGS reads to support all 14 ITD predictions.
SR methods require multiple reads to support an event at (nearly) a single nucleotide location.
Data analysis code written in R was used to calculate the percentage of support (%S) for each variant, using gapped reads to support alternative donor or acceptor sites and non-gapped reads to support retention of introns.
If the branch is due to an error we expect most reads to support the higher coverage neighbor, k a.
The criterion for alternative splicing was more than 10 reads to support the existence of the alternative exon-exon junction, and pair-sequences of these reads were also aligned to the same reference to avoid the influence of heteroduplex.
In order to differentiate sequencing errors from mutations, we used three thresholds to filter out unreliable mutation results: (1) we required at least five reads for each mutation; (2) average quality of each mutation had to be higher than 20; (3) there had to be at least one pair of mate-pair reads to support.
In addition, we considered those AS events that were uniquely identified in the control or the 50, 150 or 300 mM NaCl treatments significant if there were at least five junction reads to support and if the p value of these events was assigned to equal zero.
After filtering the splice junctions by two criteria (for details, see Materials and Methods) - an overhang size of more than 20 bp and at least two reads to support the splice junctions - a junction data set of 397,321 confident junctions that we believe to be true splice junctions was obtained.
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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