Categories
Tag: jbrowse
Visualization of maf alignments in JBrowse
Visualization of maf alignments in JBrowse 2 I have created something like this using a jbrowse plugin github.com/cmdcolin/mafviewer Update: added some optimizations, did some sanity checking, tested on 99 vertebrate alignments Feel free to give it a try and provide feedback! Note: my original answer linked to multibigwig plugin random…
BAM file read stats (A/T/C/G/ins/del) for each base position
BAM file read stats (A/T/C/G/ins/del) for each base position 2 Hi all, I have a bunch of Oxford Nanopore reads with a reference fasta. Wondering if anyone knows of any software / packages that would create some kind of csv or txt file that takes each base position in the…
“Simplifying” a very fragmented genome for visualisation?
“Simplifying” a very fragmented genome for visualisation? 3 Hi there, I have a very fragmented reference genome that I want to visualize (with jbrowse or similar) This is the paper for the genome: link Here the genome can be found: link2 Here are the quast statistics: ######## QUAST Results ########…
How to Replicate JBrowse Plot
How to Replicate JBrowse Plot 1 Hi everyone, I am a junior bioinformatician who is relatively new to genome browsers. I have recently been unsuccessfully attempting to create a graphic similar to the one below but for a different dataset. I am especially interested in how I could replicate the…
SARS-CoV-2 Viral Sample Alignment and Variant Visualization
There is a growing need for undergraduate students to learn cutting-edge concepts in genomics data science, including performing analysis on the cloud instead of a personal computer. This lesson aims to introduce a mutant detection bioinformatics pipeline based on a publicly available genetic sample of SARS-CoV-2. Students will be introduced…
synteny viewer
synteny viewer 1 I have synteny result file in “.collinearity” format. I want map synteny for only my gene of interest. Please suggest me any software which can map synteny for selected gene. comparative-genomics synteny • 85 views I compile a large list of visualization tools, here are all tools…
The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation
Hunt, T. et al. A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation. Science 318, 1913–1916 (2007). Article ADS CAS PubMed Google Scholar Crowson, R. A. The phylogeny of coleoptera. Annu. Rev. Entomol. 5, 111–134 (1960). Article Google Scholar Darwin, C. The Descent of Man, and Selection…
Bioinformatics Analyst job with Cincinnati Children’s- Bioinformatics
Expected Starting Salary Range: 27.60 – 35.28 SUBFUNCTION DEFINITION: Bioinformatics applies biology, computer science, data science, and statistics to analyze and interpret biological and clinical data. REPRESENTATIVE RESPONSIBILITIES Management and “wrangling” of genomic data. Help manage Xenopus genomes and participate in genome annotation and gene nomenclature. Perform gene orthology…
The Biostar Herald for Monday, May 01, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
Maker Gff3 file issues
Maker Gff3 file issues 1 Hi community, This is really a technical question, I hope it is OK to post it here… I am trying to import the gff3 file from Maker to my Jbrowse to view the annotations. I am using the maker2jbrowse script and getting constant errors. There…
Sequence statistics to report viruses (or bacteria and fungi) using Nanopore for diagnostic purpose
Sequence statistics to report viruses (or bacteria and fungi) using Nanopore for diagnostic purpose 0 Hello, Currently, our diagnostic lab uses nanopore sequencing for virus detection. Sometimes, we are in the grey zone while assigning a specific virus species. Also, not all viruses are equally represented in the NCBI databases….
Mapping a small number of contigs to a reference subsequence
Mapping a small number of contigs to a reference subsequence 1 Hello, Is there a method or a tool to align/map a small number of contigs (obtained with Canu) to a subsequence extracted from a reference genome ? For example,in a similar way to reads to reference assembly (using bwa…
NODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis
NDX is a heterochromatin-associated factor To understand the genome-wide regulatory roles of NDX, we first analyzed its genomic distribution. For this, we performed chromatin immunoprecipitation sequencing (ChIP-seq) in 10-day old Arabidopsis seedlings expressing N-terminally and C-terminally tagged NDX fusion proteins (flag-NDX/ndx1-1(FRI)/flc-2 and NDX-GFP/ndx1-1(FRI)/flc-2, respectively) expressed from their endogenous promoter21,32. The…
ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes | BMC Bioinformatics
1. Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G, Goodstein DM, Elsik CG, Lewis SE, Stein L, et al. JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 2016;17:66. Article Google Scholar 2. Minio A, Lin J, Gaut BS, Cantu D. How single…
PolyAllele Detail
Polymorphism: FLAG_344G02 Name FLAG_344G02 Date last modified 2006-09-11 Aliases 344G02 Tair Accession Polymorphism:1009991284 Type insertion Insertion Type T-DNA Chromosome unknown Mutagen T-DNA insertion Mutation Site gene Associated Polymorphisms Insertion Species Variant (attribution) Length Polymorphic Sequence Polymorphism…
“Simplifing” a very fragmented genome for visualisation?
“Simplifing” a very fragmented genome for visualisation? 1 Hi there, I have a very fragmented reference genome that i want to visualize (with jbrowse or similar) this is the paper for the genome: link here the genome can be found: link2 here are the quast statistics: ######## QUAST Results ########…
Gmod linux error splicing
20-08-2021 The Generic Model Organism System Database Project (GMOD) seeks to runs well on a variety of platforms including such Unix-based systems as Linux, Solaris, a polished user interface for user support, feature requests, and bug reports. Integrated Genome Browser reveals stress-induced alternative splicing of the. Splicing is…