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For quality control, the automated segmentations and parcellations of each individual participant were manually inspected for errors before including the data for statistical analysis.
Allele calls were visually inspected for errors in automatic allele calling and corrected where deemed necessary.
Stove usage files were transferred to the field office, where they were inspected for errors and minimally processed.
Segmentation was visually inspected for errors or regions where segments were closely apposed and manually edited where necessary.
Data were double entered and cleaned, then manually inspected for errors and outlying values, which were then confirmed or corrected with original records.
Allele calls and genotype clusters were visually inspected for errors in automated SNP genotype clustering algorithm and corrected based on the expected segregation ratio in the RIL population [ 48].
Sequences were manually inspected for annotation errors and duplicate sequences were removed.
Based on bin map positions, all unigenes were ordered and graphical genotypes were inspected for obvious errors in unigene placement.
Genotypes of 228 sire-offspring pairs were inspected for mendelian errors (e. g. genotype AA and BB in sire and offspring, respectively).
Genotypes of sire-offspring pairs were inspected for mendelian errors (i.e., genotype AA and BB in sire and offspring, respectively) and SNP with more than 500 mendelian errors were excluded.
The contigs thus generated were screened with in-house Perl scripts to check for the low-quality regions (Phred quality values ≤ 25), and they were manually inspected for sequencing errors by using the Consed program [ 60].
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