Tag: 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 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? 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 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…

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 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…

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…

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 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 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 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 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…

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…

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…

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? 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 ########…

  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…