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Extending the reads beyond this threshold length would cause a sudden improvement in the assembly and introduce a step-wise character to the curves in Figure 5.
SISSRs (Site Identification from Short Sequence Reads) also starts by extending the reads to the estimated length of the DNA fragment, similarly as FindPeaks.
PeakSeq first constructs a similar read density map as FindPeaks by extending the reads directionally to the average length of the DNA fragments and determining their overlap along the genome.
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Recently, there have been several publications that deal with extending the read range of the UHF readers.
We extended the reads by complete random sequences with the lowest possible quality scores.
The software program readingExtension was used to extend the reads of the SAM file from approximately 51 to 400 nt (Additional file 3: TomatoProgramCode zip file).
Some authors artificially extend the reads in the 5′→3′ direction or they shift the positions of the mapped read position of the forward and reverse toward the middle of potential nucleosomes.
We have used this approach to extend the read length of SBL to thirteen base pairs in the 3' - 5' direction.
Paired-end NGS could computationally extend the read length but with a lot of practical inconvenience because of the inherent gaps.
We mapped all of the nucleosome reads from [ 52] to the human genome and then extended the read length to 150 bp to include the entire length of the nucleosome.
Extending the reading experience to the whole family can help to raise literacy levels across the entire society.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com