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More specifically, for each of these targets, we calculated the number of reads that could be mapped only to the C57BL/6 J or SPRET/EiJ genome.
Of the remaining reads, if a read could be mapped only to one genome, the allelic origin is obvious, while if a read could be mapped to both genomes with different edit distances, the strain with smaller edit distance was assigned as the allelic origin.
For each of the internal exon E, we computed percent splicing in value, PSI = ein/ ein + eout), where ein denotes the number of reads which could only be mapped to E or exon junctions containing E with an overlap of at least 6 bp, and eout denotes the number of reads which could be mapped only to exon junctions skipping E and overlap with both exons by at least 6 bp.
For each intron I, we computed percent intron retention value, PIR = iin/(iin + iout), where iin denotes the number of reads which could only be mapped to junctions between I and adjacent exons, and overlap with I by at least 6 bp, and iout denotes the number of reads which could be mapped only to exon exon junctions skipping I and overlap with both exons by at least 6 bp.
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Thus, the category "Primary amines" (CHEMONTID 0002450) has been mapped only to the equivalent ChEBI term "primary amine" (CHEBI: 32877), and not its parent.
Interestingly, for 24,847 specific probes (that is, mapped only to the intended target), the entire probe (50 bps) was in repetitive DNA.
The authors also stated that tiRNAs were mapped only to unique genomic sequences, which bias their appearances in spanions (those tiRNAs that are not located in unique genomic sequences were not reported by Taft et al)..".... Authors' response: We agree with the concerns of the referee regarding the filtering procedure.
In these mapping algorithms, there is a restriction which limits IPs to be mapped only onto single routers.
Only alignments that fitted these criteria best were chosen for future analysis to ensure that every Illumina read was mapped only once to one of the genomic reads (locations).
For the 43 SSRs derived from sorghum that were mapped, only 8 (19%) were specific to one homology group and the majority (27 markers, 63%) only generated one SD marker.
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.
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