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However, the mapping of junction reads was strongly impacted by the gene models (see Figure 3C).
Thus, the effect of a gene model on the mapping of junction reads is significantly influenced by read length.
Figure S3 quantifies the impact of a gene model on the mapping of junction and non-junction reads.
Tables S5 and S6 summarize the impact of the usage of a gene model on the mapping of junction and non-junction reads in all 16 tissue samples.
In this paper, we assessed the impact of gene models on the mapping of junction and non-junction reads, and compared the impact of genome annotation choice on gene quantification and differential analysis.
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Our research focused on: (1) comparing the coverage and incompleteness of different gene models; (2) quantifying the impact of gene models on the mapping of both junction and non-junction reads; and (3) evaluating the effect of genome annotation choice on gene quantification and differential analysis.
The mapping specificity of junction reads largely depends on the negative control database.
Interestingly, thorough mapping of neuromuscular junction (NMJ) denervation patterns in the SOD1G93A mouse model of ALS revealed increased susceptibility of glycolytic fibers to undergo denervation.
The impact of a gene model on mapping of non-junction reads is different from junction reads.
From GSSP analysis, we found one peptide mapping to junction of second exon and second intron and two peptides mapping to the second intron.
454 and RACE reads were mapped to the Vitis vinifera L. genome sequence using preliminary Blast searches and fine mapping of splice junctions was performed using SPIDEY [ 57] with default settings for plant sequences.
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