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Sequence reads obtained from RNA-seq experiments were mapped onto the same reference genome (NC_000913.2) using bowtie41 with the maximum insert size of 1000 bp, and 2 maximum mismatches after trimming 3 bp at 3′ ends.
Alternatively, cloning of viral genomes in fosmids has been successfully used for obtaining complete marine viral genomes10,11, but this approach is limited by the maximum insert size that is allowed by the cloning vectors (genomes <40 kb).
Heinz with a maximum insert size of 750 bp (50% deviation), reporting at most 30 hits and removing PCR duplicates.
The only parameter that was varied when mapping was the -i option to specify the maximum insert size.
First, we identified heterozygous germline SNPs that were less than the maximum insert size away from a given mutation on the relevant chromosome (700bp in this sample).
Mapping was done with BWA [ 73] aligning pairs of reads and allowing maximum insert size to 500 bp and keeping only reads with mapping quality higher than 20.
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Minimum and maximum insert sizes were set at 150 bp and 350 bp, respectively, to account for variation in insert size within and across samples.
While these techniques clearly demonstrate the power of larger distance information, most do have limitations that could interfere with comprehensive analysis (e.g., maximum insert sizes of ~10 kb [ 17, 19], potential biases introduced by enzymatic digestions [ 18], and relatively laborious or costly approaches that can only produce single fixed insert size libraries [ 20, 21]).
Maximum and minimum insert size of 500 bp and 0 bp respectively were selected for mapping.
The overgos were ordered in 96-well plates from Sigma-Genosys, maximizing the distance between overgos in a 12 × 12 pooling array to a distance equalling or exceeding the maximum BAC clone insert size.
Thus one may conclude that the ratio of the maxima in the insert size distributions of BAC-clones equals the ratio of genome sizes.
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