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However, both sequences may map equally well to both positions in base space.
The assembled contigs map equally well to the 3′ and 5′ ends of AstV-SG and the 3′ end of HMO-C (genbank accession numbers GQ891990 and GQ415662).
Overall, about 87 91 % of reads uniquely map to genomic regions, while approximately 3.5%% of reads map equally well to multiple locations.
The primary complication of short read mapping is that a read may map equally well or nearly equally well to multiple positions because of repetitive sequences in the genome.
Furthermore, while most reads map equally well both places, there were 166 reads that mapped only to the official precursor, and only three that mapped exclusively to the alternative precursor.
Reads that map equally well at multiple locations or fail to map at all are given mapping qualities of 0. For many experiments, alignments below a certain mapping quality, usually values of 20, 30 or 40, are filtered out.
Similar(51)
One drawback of using uniquely-mapped RNA-seq reads for expression analysis is that any read which maps equally well to identical regions in different genes is discarded, potentially resulting in an underestimation of the expression levels of highly similar genes [ 21].
For alignments to the IAdb, Novoalign (http://www.novocraft.com/) was used (version 2.05.20 [-o SAM -r A -R 0, default options] (http://www.novocraft.com/) which reports all locations and genomes mapped equally well by a given read pair.
Reads mapping equally well to two positions were assigned randomly.
Moreover, reads that mapped equally well to more than 40 genomic locations were discarded.
Reads mapping equally well to both genotype-specific references were assigned to a "both" category.
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