Salmon provides fast and bias-aware quantification of transcript expression

Patro, Rob; Duggal, Geet; Love, Michael I.; Irizarry, Rafael A.; Kingsford, Carl

doi:10.1038/nmeth.4197

Cited by 7,671 publications

(5,700 citation statements)

References 28 publications

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“…Aligned reads showed an average mapping rate of 61%. Transcript quantification was performed using Salmon version 0.7.1 using quasimapping-based mode with automated libtype detection (56,57). TPM was computed for each gene by aggregating transcript counts and normalizing by total number of mapped reads.…”

Section: Methodsmentioning

confidence: 99%

PMP22 antisense oligonucleotides reverse Charcot-Marie-Tooth disease type 1A features in rodent models

Zhao¹,

Damle²,

Ikeda-Lee³

et al. 2017

Journal of Clinical Investigation

123

117

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Section: Methodsmentioning

confidence: 99%

PMP22 antisense oligonucleotides reverse Charcot-Marie-Tooth disease type 1A features in rodent models

Zhao¹,

Damle²,

Ikeda-Lee³

et al. 2017

Journal of Clinical Investigation

123

117

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“…Alignment of the reads to the reference was done using BWA-MEM using the same settings as applied for the variant calling. Transcripts per million values were extracted from the BWA-aligned reads using Salmon (Patro et al, 2017). Transcripts with expression levels greater than three counts in three libraries were retained.…”

Section: Transcriptional Profilingmentioning

confidence: 99%

Six-Rowed Spike3 (VRS3) Is a Histone Demethylase That Controls Lateral Spikelet Development in Barley

et al. 2017

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The complex nature of crop genomes has long prohibited the efficient isolation of agronomically relevant genes. However, recent advances in next-generation sequencing technologies provide new ways to accelerate fine-mapping and gene isolation in crops. We used RNA sequencing of allelic six-rowed spike3 (vrs3) mutants with altered spikelet development for gene identification and functional analysis in barley (Hordeum vulgare). Variant calling in two allelic vrs3 mutants revealed that VRS3 encodes a putative histone Lys demethylase with a conserved zinc finger and Jumonji C and N domain. Sanger sequencing of this candidate gene in independent allelic vrs3 mutants revealed a series of mutations in conserved domains, thus confirming our candidate as the VRS3 gene and suggesting that the row type in barley is determined epigenetically. Global transcriptional profiling in developing shoot apical meristems of vrs3 suggested that VRS3 acts as a transcriptional activator of the row-type genes VRS1 (Hv.HOMEOBOX1) and INTERMEDIUM-C (INT-C; Hv.TEOSINTE BRANCHED1). Comparative transcriptome analysis of the row-type mutants vrs3, vrs4 (Hv.RAMOSA2), and int-c confirmed that all three genes act as transcriptional activators of VRS1 and quantitative variation in the expression levels of VRS1 in these mutants correlated with differences in the number of developed lateral spikelets. The identification of genes and pathways affecting seed number in small grain cereals will enable to further unravel the transcriptional networks controlling this important yield component.

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“…We adopted the Salmon [20] algorithm to estimate the relative TE abundance from a given RNA-seq sample. Salmon enables a fast and accurate quantification of TE expression from RNA-seq reads with a light-weight mapping, online initial expression estimation phase, and offline inference for the estimation refinement.…”

Section: Salmon Quantification Algorithmmentioning

confidence: 99%

“…Toward this end, we developed a new pipeline called SalmonTE. It deploys a low time-complexity quantification method, Salmon, 20 and contains various statistical models for TEs quantification. Moreover, SalmonTE provides a rich set of built-in functions for data pre-processing from raw FASTQ files.…”

Section: Introductionmentioning

confidence: 99%

An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data

et al. 2017

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Transposable elements (TEs) are DNA sequences which are capable of moving from one location to another and represent a large proportion (45%) of the human genome. TEs have functional roles in a variety of biological phenomena such as cancer, neurodegenerative disease, and aging. Rapid development in RNA-sequencing technology has enabled us, for the first time, to study the activity of TE at the systems level.However, efficient TE analysis tools are not yet developed. In this work, we developed SalmonTE, a fast and reliable pipeline for the quantification of TEs from RNA-seq data. We benchmarked our tool against TEtranscripts, a widely used TE quantification method, and three other quantification methods using several RNA-seq datasets from Drosophila melanogaster and human cell-line. We achieved 20 times faster execution speed without compromising the accuracy. This pipeline will enable the biomedical research community to quantify and analyze TEs from large amounts of data and lead to novel TE centric discoveries.

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Salmon provides fast and bias-aware quantification of transcript expression

Cited by 7,671 publications

References 28 publications

PMP22 antisense oligonucleotides reverse Charcot-Marie-Tooth disease type 1A features in rodent models

PMP22 antisense oligonucleotides reverse Charcot-Marie-Tooth disease type 1A features in rodent models

Six-Rowed Spike3 (VRS3) Is a Histone Demethylase That Controls Lateral Spikelet Development in Barley

An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data

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