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For multiple readings, the most abnormal reading was utilized.
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The directionality of the reads was utilized to refine the peak boundaries.
The default two-mismatch threshold was applied along with "–m 1" reporting mode to ensure that only unique, confidently mapped reads were utilized.
The metagenomic reads were utilized without prior assembly software analysis by the COMPAREADS software (Maillet et al. 2012).
These high quality reads were utilized for de novo transcriptome assembly following Velvet_1.2.10 and Oases_0.2.08 software packages [ 32, 33].
The trimmed mate pair reads were utilized in SSPACE 2.0 (Boetzer et al. 2011) to scaffold the mitochondrial de novo contigs.
Based on the initial mapping, the paired-end sequences with one mapped and one unmapped reads are utilized for remapping using pattern growth.
As a result, 95.4% of the reads could be aligned back with no more than one mismatch, and the average coverage calculated according to these was 115.2, which demonstrated that almost all reads were utilized for the de novo assembly.
In a few cases, only partial K-mers from the reads are utilized for the sequence assembly, which results in the assembled sequences not supported by the underlying reads.
In drawing the distribution of sense and antisense mapped reads around TSSs, we eliminated the furthest-upstream reads composing the transcript-enriched regions because these reads were utilized for the adjustment of the genomic location of TSSs that resulted in the intentional overrepresentation of read enrichment at the TSSs.
Only spacer combinations that were present in 60%% of the reads were utilized to reconstruct CRISPR loci, while reads that had similar CRISPR spacers within a subject with their order altered were discarded, as they may represent lesser abundant CRISPR loci or could occur from PCR amplification artifacts.
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