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when you're there to watch your kid in a school assembly... a bunch of strange kids walk in... and turns out you're in the WRONG assembly.
Various reasons may explain this bias including the low sequencing depth, locally wrong assembly or mapping bias.
Chromosome 4 has short TRPC-21A array in silico (Table 3) but it lacks any signal, probably due to the wrong assembly.
This example shows that neglecting the evolutionary information and looking only at the numerical scores from the prediction servers, it would be very easy to choose a wrong assembly.
However, considering that the distance of two reads of paired-end was utilized to assemble the sequence by the software, there is an inaccurate distance between two paired-end reads with a length smaller than 90 bp, which may lead to a wrong assembly.
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Thus, using gene containing regions as a measure we found no evidence for wrong assemblies indicated by missing exons, wrong exon order or orientation (flipped/reverse exons).
Wrong assemblies in regions harboring such elements typically can occur in two ways: (I) Sequences derived from different copies of the repeat "collapse" into one single region, finally "shortening" the consensus sequence (shown for BAC 711N16 in Fig. 5B, D).
Four out of the five sequence parts affected by wrong assemblies in set 2 were identical to those in set 1 indicating that always the same repetitive structures were the underlying cause.
If there were more than one disease gene in the ICCA region, determining a single and consensus critical region could lead to dramatic errors – notwithstanding artifacts of wrong genome assembly.
When something went wrong with the assembly, they could diagnose the problem swiftly, by consulting the data.
If something goes wrong on an assembly line, any worker can push a button and hold things in place until the problem is resolved.
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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