Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ultraplex: An ultra-fast, flexible, all-in-one fastq demultiplexer

ABSTRACT: Ultraplex: An ultra-fast, flexible, all-in-one fastq demultiplexer

PROVIDER: PRJEB44738 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR5872990.fastq.gz	Fastqsanger.gz
	ERR5873000.fastq.gz	Fastqsanger.gz
	ERR5873010.fastq.gz	Fastqsanger.gz
	ERR5873020.fastq.gz	Fastqsanger.gz
	ERR5872991.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 31

Similar Datasets

Ultraplex: An ultra-fast, flexible, all-in-one fastq demultiplexer

Project description:An Illumina sequencing lane for testing our demultiplexer, named Ultraplex, which splits a raw FASTQ file containing barcodes either at a single end or at both 5’ and 3’ ends of reads, trims the sequencing adaptors and low quality bases, and moves unique molecular identifiers (UMIs) into the read header, allowing subsequent removal of PCR duplicates. Ultraplex is able to perform such single or combinatorial demultiplexing on both single- and paired-end sequencing data, and can process an entire Illumina HiSeq lane, consisting of nearly 500 million reads, in less than twenty minutes.

2021-05-06 | E-MTAB-10349 | biostudies-arrayexpress

Ultra-fast deep-learned pediatric CNS tumor classification

Project description:Ultra-fast deep-learned pediatric CNS tumor classification

| PRJNA996977 | ENA

Ultraplex: A rapid, flexible, all-in-one fastq demultiplexer.

Project description:Background: The first step of virtually all next generation sequencing analysis involves the splitting of the raw sequencing data into separate files using sample-specific barcodes, a process known as "demultiplexing". However, we found that existing software for this purpose was either too inflexible or too computationally intensive for fast, streamlined processing of raw, single end fastq files containing combinatorial barcodes. Results: Here, we introduce a fast and uniquely flexible demultiplexer, named Ultraplex, which splits a raw FASTQ file containing barcodes either at a single end or at both 5' and 3' ends of reads, trims the sequencing adaptors and low-quality bases, and moves unique molecular identifiers (UMIs) into the read header, allowing subsequent removal of PCR duplicates. Ultraplex is able to perform such single or combinatorial demultiplexing on both single- and paired-end sequencing data, and can process an entire Illumina HiSeq lane, consisting of nearly 500 million reads, in less than 20 minutes. Conclusions: Ultraplex greatly reduces computational burden and pipeline complexity for the demultiplexing of complex sequencing libraries, such as those produced by various CLIP and ribosome profiling protocols, and is also very user friendly, enabling streamlined, robust data processing. Ultraplex is available on PyPi and Conda and via Github.

| S-EPMC8287537 | biostudies-literature

FLASH: ultra-fast protocols to identify RNA-protein interactions in cells

Project description:FLASH: ultra-fast protocols to identify RNA-protein interactions in cells

| PRJNA484982 | ENA

FLASH: ultra-fast protocols to identify RNA-protein interactions in cells

Project description:FLASH: ultra-fast protocols to identify RNA-protein interactions in cells

| PRJNA495755 | ENA

FLASH: ultra-fast protocols to identify RNA-protein interactions in cells

Project description:Determination of the in vivo binding sites of RNA-binding proteins (RBPs) is paramount to understanding their function and how they affect different aspects of gene regulation. With hundreds of RNA-binding proteins identified in human cells, a flexible, high-resolution, high-throughput, highly multiplexible and radioactivity-free method to determine their binding site has not been described to date. Here we report FLASH (Fast Ligation of RNA after some sort of Affinity Purification for High-throughput Sequencing), which uses a special adapter design and an optimized protocol to determine protein-RNA interactions in living cells. We demonstrate the flexibility, speed and versatility of FLASH by using it to determine binding sites of both tagged and endogenously expressed proteins under diverse conditions. The entire FLASH protocol, starting from cells-on-plates to a sequencing library, takes 1.5 days.

2019-10-01 | GSE121115 | GEO

FLASH: ultra-fast protocols to identify RNA-protein interactions in cells

2019-08-01 | GSE118265 | GEO

FLARE: A fast and flexible peak-calling pipeline for identifying RNA editing foci

Project description:FLARE: A fast and flexible peak-calling pipeline for identifying RNA editing foci

| PRJNA889435 | ENA

LCLF1.0 fastq-Files

Project description:LCLF1.0 fastq-Files

| PRJNA928832 | ENA

LCLF1.0 fastq-Files

Project description:LCLF1.0 fastq-Files

| PRJNA928833 | ENA