Results for "NGS"
Tags
How to extract 50% of the reads?
I would like to extract a subset of PE reads (50%) and store them in seperate files. It should be in both way "split by middle" or "random". Is there any way to achieve it?Tags: Reads, NGS, PE, Extract
2832 days ago
- I am doing megablast of a contig against NR database, but unable to understand this -outfmt '6 qseqid staxids qstart qend sstart send qseq sseq evalue length' Can you please help me to undestand all these.
Tags: Blastn, BLAST, Nucleotide, Alignment, Database, NR, Contig, NGS
2891 days ago
Linux command line exercises for NGS data processing
The purpose of this tutorial is to introduce students to the frequently used tools for NGS analysis as well as giving experience in writing one-liners. Copy the required files to your current directory, change directory (cd) to the linuxTutorial folder, and do all the processing inside: [uzi@qui...Tags: Bioinformatics, Tutorial, Genome, NGS, Pipelines
2889 days ago
- SAMtools: Primer / Tutorial by Ethan Cerami, Ph.D.keywords: samtools, next-gen, next-generation, sequencing, bowtie, sam, bam, primer, tutorial, how-to, introductionRevisions 1.0: May 30, 2013: First public release on biobits.org. 1.1: July 24, 2013: Updated wi...
Tags: Bioinformatics, NGS, Sequence, Samtools, Primer, Tutorial
2888 days ago
- Reads simulator Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing errors. It does not generate INDEL sequencing errors...
Tags: Bioinformatics, NGS, Reads, Silulator, INDEL, SNPs, Simulation
2888 days ago
- Decoding SAM flags This utility makes it easy to identify what are the properties of a read based on its SAM flag value, or conversely, to find what the SAM Flag value would be for a given combination of properties. To decode a given SAM flag value, just enter the number in the field below. The...
Tags: Bioinformatics, SAM, Flags, NGS
2882 days ago
- _A5-miseq_ is a pipeline for assembling DNA sequence data generated on the Illumina sequencing platform. This README will take you through the steps necessary for running _A5-miseq_. Point to note: There are many situations where A5-miseq is not the right tool for the job. In order to produce ...
Tags: Bioinformatics, Analysis, NGS, A5-miseq, NGOPT Assembler, Genome
2832 days ago
- alignment: the mapping of a raw sequence read to a location within a reference genome. The mapping occurs because the sequences within the raw read match or align to sequences within the reference genome. Alignment information is stored in the SAM or BAM file formats. bcftools: a set of companio...
Tags: Bioinformatics, Glossary, NGS
2884 days ago
- Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA...
Tags: Bioinformatics, Analysis, Visualization, Chromatin, NGS, HiC
2884 days ago
