Results for "micro RNA"
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bpRNA: large-scale automated annotation and analysis of RNA secondary structure
bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise,...ch such structural feature. The bpRNA code is written in perl and r...at http://github.com/hendrixlab/bpRNA....2175 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
git clone https://github.com/lh3/minimap2 cd minimap2 &am...nomic paired-end reads ./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam #...-uf ref.fa reads.fa > aln.sam # Nanopore Direct RNA-seq ./minimap2 -cx asm5 asm1...2147 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
With increased availability of de novo assembly algorithms...a transcriptome assembly algorithm that recovers alternatively spliced isoforms and expression levels while utilizing as many RNA-Seq libraries as possible tha...2134 days ago
- ChopStitch is a new method for finding putative exons and...identifies exon-exon boundaries in de novo assembled RNA-seq data with the help of a B...r assembly errors, haplotype variations, or putative RNA editing events. The primary o...
2134 days ago
RNA-seq Analysis Workshop Course Materials
RNAseq can be roughly divided into two "ty...nome exists for a species for which an RNAseq experiment is performed. I...using de novo approaches. This type of RNAseq is as much of an art as we...on the Reference genome-based type of RNA seq. http://chagall.med.co...2134 days ago
REVIGO: Reduced Visualize gene ontology
REViGO can take long lists of Gene Ontology terms and summarize them by removing redundant GO terms. The remaining terms can be visualized in semantic similarity-base...2106 days ago
- Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Ea...nto account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate i...
2091 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Choosing whether to use second or third generation sequencing platforms can lead to t...NA-seq BAC clones (CH17-157L1 and CH17-227A2), and human brain cerebellum polyA RNA-seq, we show that Hercules-co...2086 days ago
SimLoRD: A read simulator for third generation sequencing reads
SimLoRD is a read simulator for third generation sequencing reads and is...for genomic DNA), sampling from an existing FASTQ file (typical for RNA), sampling from a a text file with integers (RNA), or using a fixed length Qu...2084 days ago
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragment...uld utilize Illumina Paired-end RNA-sequencing reads from target...provides another practical alternative to existing mate-pair_bas...regions (for instance, circRNA).2068 days ago
