Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut
نویسندگان
چکیده
منابع مشابه
Evaluation of de novo transcriptome assemblies from RNA-Seq
For simplicity, we assume that RNA-Seq reads are sequenced uniformly across the transcriptome. In addition, we only consider fixed length single-end RNA-Seq reads. We denote the read length as L. Given a set of MT transcripts, we denote the relative expression levels as τ = (τ1, τ2, . . . , τMT ), the read generating probabilities as Θ = (θ0, θ1, . . . , θMT ) and the expected read coverage as ...
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Background Spittle bugs and sharpshooters are well-known xylem sap-feeding insects and vectors of the phytopathogenic bacterium Xylella fastidiosa (Wells), a causal agent of Pierce's disease of grapevines and other crop diseases. Specialized feeding on nutrient-deficient xylem sap is relatively rare among insect herbivores, and only limited genomic and transcriptomic information has been genera...
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TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only the sequenced reads and the assembly as input, we show that multiple common artifacts of de novo transcriptome assembly can be readily detected. These include chimeras, structural errors, incomplete assembly, and base errors. TransRate evaluates these errors to produce a diagnostic quality ...
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BACKGROUND Nicotiana benthamiana is an allo-tetraploid plant, which can be challenging for de novo transcriptome assemblies due to homeologous and duplicated gene copies. Transcripts generated from such genes can be distinct yet highly similar in sequence, with markedly differing expression levels. This can lead to unassembled, partially assembled or mis-assembled contigs. Due to the different ...
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ژورنال
عنوان ژورنال: PLOS ONE
سال: 2020
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0232005