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Analysis pipelines rely on mapping the resulting fragments to a reference genome, if available.
By mapping the resulting short sequencing reads onto the reference genome, the expression levels of genes relative to the condition of interest or absolute levels can be quantified [ 9, 11].
After mapping the resulting contigs back to the reference with Blasr, we determine whether the remapped sequence is consistent with the size and type of the corresponding predicted SV event.
Due to the nature of mapping, the resulting two categories of mapped loci differ in the way they affect the phenotypic variation, either conditional on the second trait (rQTL) or conditional on the genotype at the second locus (intQTL).
The position of insertions can be determined by amplifying DNA flanking the provirus using linker-mediated PCR and mapping the resulting sequences onto the genome.
The method consists in sequencing the two ends of DNA segments of known size from a given individual and mapping the resulting reads to a reference genome (see the accompanying review by Escaramís et al. [ 12]).
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We also mapped the resulting center sequences to their nearest template sequences to access the accuracy of the results.
We mapped the resulting paired-end reads to the reference genome sequence to identify sequence variation (see online supplementary methods).
We then mapped the resulting 6,368,000 sequence reads from a single sequencing lane to the human genome (see Methods).
We mapped the resulting FASTQ files using bowtie, version 0.12.7 [ 81], allowing for single hits (−m 1).
mapping the results of the search strategy in a flowchart.
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