Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparison of splicing tools

ABSTRACT: Comparison of splicing tools

PROVIDER: PRJNA675664 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13013260.fastq.gz	Fastqsanger.gz
	SRR13013261.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Comparison of splicing tools

Project description:Study that compares three commonly used event-based differential splicing tools: rMATS, MISO, and SUPPA2

2021-04-01 | GSE161144 | GEO

Comparison of tools for identification of rRNA Modifications

Project description:Comparison of tools for identification of rRNA Modifications in Escherichia coli using Oxford Nanopore direct RNA Sequencing

| PRJEB58726 | ENA

Systematic comparison of tools used for m6A mapping from nanopore direct RNA sequencing

Project description:Systematic comparison of tools used for m6A mapping from nanopore direct RNA sequencing

| PRJNA801506 | ENA

Comparison of organoids from Menstrual Fluid and Hormone-treated Endometrium: Novel tools for Gynaecological Research

Project description:Comparison of organoids from Menstrual Fluid and Hormone-treated Endometrium: Novel tools for Gynaecological Research

| PRJNA780602 | ENA

From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools

Project description:Comparison of different tools for metagenome taxonomic classification

| PRJEB55832 | ENA

Analysis of Human Serum O-glycoproteomics data with Glycoproteomic Tools

Project description:Based on our previous O-Search strategy, we have developed a new search method, O-Search-Pattern, to process searching for O-glycopeptide. In comparison of analyzing our human serum dataset generated from optimized energy, our new method can generate more GPSMs glycopeptide sequences than currently state-of-the-art search tools.

2023-05-31 | PXD039079 | JPOST Repository

Evaluation of CRISPR gene-editing tools in zebrafish

Project description:CRISPR tools for zebrafish

| PRJEB39643 | ENA

Systematic comparison of tools used for m6A mapping from nanopore direct RNA sequencing

Project description:State-of-the-art algorithms for m6A detection and quantification via nanopore direct RNA sequencing have been continuously developed, little is known about their capacities and limitations, which makes a comprehensive assessment in urgent need. Therefore, we performed comprehensive benchmarking of 10 computational tools relying on current-based and base-calling “errors” strategies for m6A detection by nanopore sequencing.

2023-03-01 | GSE195618 | GEO

matchSCore: Matching Single-Cell Phenotypes Across Tools and Experiments

Project description:Single-cell transcriptomics allows the identification of cellular types, subtypes and states through cell clustering. In this process, similar cells are grouped before determining co-expressed marker genes for phenotype inference. The performance of computational tools is directly associated to their marker identification accuracy, but the lack of an optimal solution challenges a systematic method comparison. Moreover, phenotypes from different studies are challenging to integrate, due to varying resolution, methodology and experimental design. In this work we introduce matchSCore (https://github.com/elimereu/matchSCore), a measure to fastly match cell populations across tools, experiments and technologies. We compared 14 computational methods and evaluated their accuracy in clustering and gene marker identification in simulated data sets. Further, we used matchSCore to project cell type identities across mouse or human cell atlas projects. Despite originated from different technologies, cell populations could be matched across datasets, allowing the assignment of clusters to reference maps and their annotation.

2021-04-30 | GSE114138 | GEO

High-throughput sequencing of Arabidopsis thaliana pollen cDNA uncovers novel transcription and alternative splicing

Project description:Pollen grains of Arabidopsis thaliana contain two haploid sperm cells enclosed in a haploid vegetative cell. Upon germination, the vegetative cell extrudes a pollen tube that carries the sperm to an ovule for fertilization. Knowing the identity, relative abundance, and splicing patterns of pollen transcripts will improve understanding of pollen and allow investigation of tissue-specific splicing in plants. Most Arabidopsis pollen transcriptome studies have used the ATH1 microarray, which does not assay splice variants and lacks specific probe sets for many genes. To investigate the pollen transcriptome, we performed high-throughput sequencing (RNA-Seq) of Arabidopsis pollen and seedlings for comparison. Gene expression was more diverse in seedling, and genes involved in cell wall biogenesis were highly expressed in pollen. RNA-Seq detected at least 4,172 protein coding genes expressed in pollen, including 289 assayed only by non-specific probe sets. Additional exons and previously unannotated 5’ and 3’ UTRs for pollen-expressed genes were revealed. We detected regions in the genome not previously annotated as expressed; 14 were tested and 12 confirmed by PCR. Gapped read alignments revealed 1,908 high-confidence new splicing events supported by 10 or more spliced read alignments. Alternative splicing patterns in pollen and seedling were highly correlated. For most alternatively spliced genes, the ratio of variants in pollen and seedling was similar, except for some encoding proteins involved in RNA splicing. This study highlights the robustness of splicing patterns in plants and the importance of on-going annotation and visualization of RNA-Seq data using interactive tools such as Integrated Genome Browser.

2013-05-25 | E-MTAB-4242 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data