Tag: IGV

Hey, is there a way to make all bases that are from the same read in one vertical line using mpileup? So making this chr2 96 C 5 .,.,, chr2 97 A 4 .,., chr2 98 C 6 .,.,,, chr2 99 C 8 .,.,,,.. chr2 00 A 9 .,,,..,,. chr2…

Loss of ASH2L prevents cell proliferation We have studied the molecular and cellular consequences of Ash2l loss in mouse embryo fibroblasts (MEFs) with floxed Ash2l alleles and an inducible Cre-ER recombinase (iMEF-Ash2lfl/fl-Cre-ER). While the knockout of Ash2l was rapid, the downstream effects, including the decrease in promoter-associated H3K4me3, altered gene…

Whole-genome sequencing (WGS) analysis of early and advanced adenocarcinomas Whole-genome short read and long read sequencing datasets of 76 lung cancer specimens were analyzed. The datasets included newly generated data for 48 early small-sized lung adenocarcinoma cases (collectively called “Early-Ad” hereafter). These cases included 26 AIS (9 and 17 cases…

UPMC Presbyterian is hiring a full-time Bioinformatics Scientist to support the Molecular & Genomic Pathology Lab! This role will be scheduled for daylight shifts, Monday-Friday. The Molecular & Genomic Pathology Laboratory is a dynamic, state-of-the-art clinical laboratory that prides itself on delivering the highest quality of patient care through cutting-edge…

Merge overlapping paired end reads from BAM file. 0 Hi everyone, Using Trimmomatic and then HISAT2, I have aligned 300 RNA fastq samples (NovaSeq6000, RNA sequencing, paired-end, 150bp sequencing). I have found a percentage of overlapping paired end reads (read through) in the 300 .bam files. I found the overlaps…

Variant missing in WGS sample 1 Hi, I have processed a WGS sample including alignment (bwa-mem2), variant calling (GATK HaplotypeCaller) and annotation (ANNOVAR). In the annotated file, a variant fitting the phenotype was identified. However, on visualizing the bam in IGV, this variant was not there. What could be the…

Mouse genetic models The ThrbHAB allele expresses TRβ proteins (TRβ1 and TRβ2) fused to a peptide with a hemagglutinin (HAx2) tag and a site for biotinylation by prokaryotic BirA ligase, modified from a published tag30. The tag was inserted at the endogenous Thrb gene by homologous recombination in W9.5 (129/Sv)…

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, cmdcolin, and was edited by…

Annotation Visualization IGV 0 I was wondering if anyone had any insight into visualizing a GFF in IGV. I have some reads aligned to a reference sequence to visualize coverage and would like to include the annotations in that visualization as well for ease of presentation. I cant seem to…

sequencing data from different samples in the Integrative Genome Viewer (IGV) 0 Greetings, I need to carry out an activity for my master’s degree in Biostatistics and Bioinformatics that consists of viewing sequencing data from different samples in the Integrative Genome Viewer (IGV) in order to analyze alignments and variants….

In what case there are RR reads but no LL reads when detect inversions using IGV? 0 Hi all, From Integrative Genomics Viewer User Guide, when an inversion shows up in paired-end reads, there should be both RR reads and LL reads. As shown below. When I use the orientation…

Visualize and explore eventalign data against reference 0 Hi all, Is anyone aware of a tool (GUI or python/R/bash package) to explore eventalign nanopore data (or fast5 raw data) with the corresponding alignment to a reference genome? Kind of like viewing how reads in a bam file align against a…

Introduction Patients with persistent, recurrent, or metastatic (P/R/M) cervical carcinoma respond poorly to treatment despite the best available therapeutic regimens, with a 5-year survival of 17%.1 Most of them are heavily pretreated with chemotherapy and/or radiotherapy, and many patients experience complications related to treatment or advanced disease, which exclude them…

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…

Find all locations of aligned reads with MQ (Mapping Quality) = 0. 1 I have white reads in BAM file with MQ = 0. I know that it means that reads align to multiple locations. I know location of one align, but can i find another location/locations in IGV? If…

. 2023 Nov 17:12:RP89338. doi: 10.7554/eLife.89338. Affiliations Expand Affiliation 1 Vollum Institute, Oregon Health & Science University, Portland, United States. Item in Clipboard Jimmy J Kelly et al. Elife. 2023. Show details Display options Display options Format AbstractPubMedPMID . 2023 Nov 17:12:RP89338. doi: 10.7554/eLife.89338. Affiliation 1 Vollum Institute, Oregon Health &…

This study is aimed at revealing the transgenerational effects of thia. We chose the developmental window from embryonic days 6.5 to E15.5 because of its importance in germ cell program establishment. The mice breeding was described in the Materials and Methods section “Mouse treatment and dissection.” The design of the…

UCSC Genome Browser Custom Track Blank 0 Hello, I have a bigwig (.bw) file which I can properly view on IGV. IGV makes it very difficult to edit the figure nicely so I am trying to view it in the UCSC genome browser. I uploaded my data to cyverse and…

Diffbind low p-value but high FDR 0 I guess my issue is related to this post support.bioconductor.org/p/85487/#85490. Here is the dba.report(DBA,th=1, bCounts=TRUE) results. One of the peaks clearly shows a significant difference in IGV (And we also expected it to be changed) and has a small p.vaule but the FDR…

1. Introduction Cervical cancer (CC) is the third most common cancer in women worldwide and has a high mortality rate among women. In 2008, CC was responsible for 275,000 deaths, thereby being the fourth leading cause of cancer death in females worldwide.[1,2] In China, CC is the second most…

IGV not showing bigwig track information 0 Hi there, I’m struggling to view some .bw files in IGV – however when I load .bam files into IGV (the same ones used to create the aforementioned .bw files) I do not encounter this issue. Whether I have fundamentally misunderstood what a…

Rojas, J. M. & Santos, E. Ras-Gefs and Ras Gaps. In RAS Family GTPases Vol. 4 (Springer, 2006). Google Scholar  Broek, D. et al. The S. cerevisiae CDC25 gene product regulates the RAS/adenylate cyclase pathway. Cell 48, 789–799 (1987). Article  CAS  PubMed  Google Scholar  van Dam, T. J. P., Rehmann,…

RNA-Seq with DNA contamination, any way to salvage the data? 1 Hello, My group has performed RNA-Seq using Illumina Truseq RNA Exome kit, we performed alignments with HISAT2 and we noticed that a good portion of our samples had DNA contamination. So far, I have seen a lot of discussion…

Human induced pluripotent stem cells (iPSCs) Reprogramming and Culture This study was ethically approved by the Medical Ethics Committee of Nanjing Maternal and Child Health Care Hospital (2021KY-131), and informed consents were obtained from the patient’s legal guardian as well as the healthy donors, in accordance with the Declaration of…

Introduction The non-random packaging of chromatin within the nucleus is a universal feature of eukaryotic genomes. The three-dimensional (3D) spatial organization of chromatin could be partitioned at different levels based on the interaction frequency between two given loci in the genome. Advances in sequencing technologies have led to the identification…

Primary samples and nucleic acid extraction A cohort of 48 patients diagnosed with advanced adenoma (AAD), defined by size > 20 mm, or colorectal carcinoma (CRC) were collected between 2013 and 2016. The study was approved by the institutional ethics committee of Hospital General Universitario de Alicante (Ref. CEICPI2013/01), and written informed consent…

Ethical statement Our research complies with all relevant ethical regulations, including the Declaration of Helsinki and has been approved by the Institutional Review Boards of University of Chicago, Duke University and the Alliance to Cure Cavernous Malformations. Cerebral cavernous malformation lesions All human CCM tissue specimens have been previously reported18,19…

Converting IGV to Figure using Illustrator (or other tools) 0 Hello, I am trying to use Illustrator to edit a saved IGV picture (in SVG format). Frustratingly, IGV’s saved SVG is very complicated and contains many layers and data making it difficult to edit. Has anyone experienced this and has…

Filtering vcf by strand bias / annotating strand bias on 0 Hello, I have a vcf file with a lot of variants, from Igv I can tell which variants possess strand bias. Is it possible to find a bioinformatics solution to filter out these variants? For example is there another…

Low coverage, deletion and startloss? What do we see here? 0 Hello all, we are currently not quite sure what we see here. All three are directly related to each other. Now we are wondering why the coverage across all 3 genomes is so poor, also we see a startloss…

Percentage of samples covered per region in IGV 0 Hello everyone, I was able to generate a .tdf file with multiple bam files for the coverage using an igv tool “count”. It only displays the number of reads covered in a particular region. I also want another track to show…

Confirming called variants 0 Hello, I performed whole exome analysis using GATK pipeline. After annotation of variant using annovar, I performed these steps: Filtered variants that have passed all filters Using Gnomad_exome_all, looked for variants less than 0.01 Then tried to confirm if these variants are also present in bam…

Inspiration Computational Biology allows for the intersection of biology and computing for technological innovations and optimizations in genomics, modeling systems, biology, phylogenetics, etc. In our project, we chose to focus on studying the structure and function of sequences from a community of organisms, like on human skin, in the soil,…

Hello everyone, Basically, I have clustered and annotated the barcodes in R, then I wanted to look at reads in several particular clusters in IGV. I generated a barcode list following the 10X tutorial as the picture below shown, briefly subset the clusters in R then tagged the barcodes with…

How to obtain data on the specific location of the segumental duplication. 2 I know it can be viewed from the Repeats segemental dups at the bottom of the UCSC, but I would like to view it in the IGV, not the UCSC. So I looked for the golden path…

Plant material and growth conditions Nicotiana tabacum cultivar Petit Havana was used for all experiments. The TALEN design and the TALEN-expressing line Nt-JF1006-30 were described previously19. For plant growth under sterile conditions, surface-sterilized seeds were germinated on Murashige and Skoog (MS) medium52 consisting of premixed MS salts and modified vitamins…

Visualization of Genomes 0 I’m doing a project and want to to visualize the variants’ locations on the MexR gene for Pseudomonas Aeruginosa and create plots showing the distribution of predicted functional impacts. I’m a beginner and was recommended to use IGV but I don’t know how to do this….

About IGV The Integrative Genomics Viewer (IGV) is a high-performance, easy-to-use, interactive tool for the visual exploration of genomic data. It supports flexible integration of all the common types of genomic data and metadata, investigator-generated or publicly available, loaded from local or cloud sources. IGV is available in multiple forms,…

Strong correlation exists between recombination rate and abundance and proportion of indels Whole-genome sequence data of many C. elegans wild isolates now exist. These include Illumina paired-end data of over 600 wild isolates by CeNDR, which also obtained first-generation PacBio long-read data of 14 wild isolates. Second-generation PacBio HiFi data20…

The BioNT consortium is dedicated to providing a comprehensive training program and fostering a community for digital skills relevant to the biotechnology industry and biomedical sector. With a curriculum tailored for both beginners and advanced professionals, BioNT aims to equip individuals with the necessary expertise in handling, processing, and visualising…

Dear community, I have huge BAM files (mapped using BBTools+coordinate-sorted via SAMTOOLS), which I used for variant calling. Now I would like to manually check specific positions/ variants in the mapped data using Tablet and/or IGV. Unfortunately, the BAM files are extremely large, rendering it impossible to download them from…

Siguier, P., Gourbeyre, E., Varani, A., Ton-Hoang, B. & Chandler, M. Everyman’s guide to bacterial insertion sequences. Microbiol. Spectr. 3, MDNA3-0030-2014 (2015). Article  PubMed  Google Scholar  He, S. et al. The IS200/IS605 family and “peel and paste” single-strand transposition mechanism. Microbiol. Spectr. 3, MDNA3-0039-2014 (2015). Article  ADS  Google Scholar  Kapitonov,…

Troubles launch IGV on Linux(Debian) 0 I am trying to run IGV on Debian. I have followed this steps wget data.broadinstitute.org/igv/projects/downloads/2.16/IGV_Linux_2.16.2_WithJava.zip unzip IGV_Linux_2.16.2_WithJava.zip My@machine:~/software/IGV_Linux_2.16.2$ ./igv.sh And this is the output I got WARNING: package com.sun.java.swing.plaf.windows not in java.desktop WARNING: package sun.awt.windows not in java.desktop openjdk version “11.0.13” 2021-10-19 OpenJDK Runtime…

Introduction Although protein-coding regions represent only 1–2% of the human genome, they harbour an estimated 85% of annotated pathogenic variants.1 2 Despite these numbers, genome sequencing (GS) usually achieves a higher diagnostic yield than sequencing approaches that focus on exonic regions, not least because of its more homogeneous coverage3 4…

ATAC-seq troubleshoot – Just Noise 0 Hi everyone, I have been processing paired end 150bp ATAC-seq data, but failing to get peaks at known promoters, the data just looks like noise through out. Started with QC, where reads had poly(G) towards their ends, this is known to happen in NovaSeq…

Yang, L. E. et al. Redefining Pyropia (Bangiales, Rhodophyta): Four new genera, resurrection of Porphyrella and description of Calidia pseudolobata sp. Nov. from China. J. Phycol. 56, 862–879 (2020). Article  CAS  PubMed  Google Scholar  Mumford Jr, T. F. Porphyra as Food: Cultivation and Economics in Algae and Human Affairs (ed….

1. Introduction Newborn screening (NBS) plays a vital role in healthcare systems for the prompt identification of individuals who may develop one of a set of rare, but severe health conditions [1]. In the UK, for example, dried blood spot (DBS) specimens are routinely collected at 4–5 days of age…

Design and synthesis of reference plasmid A reference construct was first designed, with the intention of optimising the production of RNA therapeutics for pre-clinical research. The coding sequence of eGFP30 was selected as a reporter in the coding region, as its protein product can be assayed simply through Flow cytometry…

Hello everyone, I’m a student in the area of genomics. I have two genome assemblies from long reads (from haploid genomes). One is the reference of the organism (K. phaffii, a yeast), which represents the wild type. The other (the query) is an assembly of an K. phaffii strain, which…

quantifying splicing transcripts for nanopore RNAseq 0 Hi all, I’m looking for some help in quantifying the number of transcripts in a virus genome from nanopore RNAseq data. I’ve currently been mapping the RNAseq data back to the reference genome using minimap, and then running Nanosplicer and stringtie to quantify…

APPLY NOW UPMC Magee-Womens Hospital is hiring a full-time Senior Genome Bioinformatics Analyst or Genome Bioinformatics Analyst to join the Genomics laboratory team! This will be a remote position. Applicants will be placed into the appropriate job title and salary based on their individual experience and education. The Genome Bioinformatics Analyst’s…

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…

samtools ampliconclip option –strand is not working? 0 I am developing a new NGS amplicon-based test. I need to mark the primers and I am using Samtools ampliconclip tool. It is working ok but I have an issue when using the -strand option. The following image shows amplicons overolapping one…

Dear all, I am using GATK (v4.1.9.0) AnnotateVcfWithBamDepth to get the DP for all variants in ClinVar VCF in a retina RNA-seq BAM file. However, the tool returns zero depth for all variants in the VCF, even though I checked multiple variants in IGV and I saw that they are…

Recapitulating a GenomeBrowser-style plot 1 I’m trying to visualize some cut&tag data, and would like to re-capitulate a plot that looks like this: The key features I’m looking for are: (1) The ability to vertically highlight regions [though I’m OK doing this in post, too] (2) The presence of tracks…

I recently performed a p300 ChIP-seq on two different genotypes. I aligned my reads using STAR aligner, and made UCSC .bedGraph files that I loaded on IGV viewer. I noticed that the reads for one of my genotypes – genotypeX (red – combined replicates; purple and pink – individual replicates)…

Error in openning FastQC 0 Hi everyone, I’m a beginner in Bioinformatics. I’ve recently used Debian 12 (VirtualBox 7.01) to practice some tools for RNA-seq analysis. I have some problems when running FastqC and IGV on the operating system. I downloaded FastQC windows/linux zip file. The scripts executed to install…

What is the common practice to view WGS data on IGV? 1 Hi, I would like to manually examine mutations on specific chromosomes in around 50 whole-genome sequencing (WGS) data samples. Each BAM file is larger than 10GB. I’m wondering about the standard approach for visualising these mutations using the…

display vcf after giraffe alignment on IGV 0 I performed Giraffe alignment to map reads to the HPRC pangenome, resulting in a gam file. Subsequently, I utilized the following commands to generate a .vcf file: Generated a pack file with the following command: ./vg pack –x hprc-v1.0-mc-grch38-minaf.0.1.gbz –g hprc1004mapped.gam >…

Extremely high ChIP-seq peak at mouse Chr2 “Gm10800” region 1 I was dealing with some CUT&TAG ChIP-seq data(for TF). After mapping and peak calling, I tried to use IGV to observe their peak distribution around the genome, and I found there are a a great number of peak/reads mapped to…

Why this alignment is shown as “Tandem Duplication”/”Translocation on the Same Chromosome” when coloring by pair orientation in IGV? 0 This alignment from illumina sequencing is arranged in a convergent form, which should be shown as a norm pair, if I understand the pair orientation schema of IGV correctly. However,…

Here are some installation instructions from a non-programming Mac Mavericks user from September 2014, that downloads and builds the BEDTools package for IGV. Download the most recent stable release of BEDTools from Github: github.com/arq5x/bedtools2/releases. For user, this was v2.21.0. Unzip the download and move entire folder to Applications. For user,…

Interpret IGV output inversion 0 Hi, I have these IGV outputs (I do not filter supplementary and secondary alignments) : I suspect a “duplicated inversion” in an other region on the same chromosome : All the soft clipped reads in the first region are found in the other one. Also,…

doi: 10.1186/s12864-023-09541-9. Affiliations Expand Affiliations 1 State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China. shaozhenyu2017@sibcb.ac.cn. 2 Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical…

Bacteria WGS via illumina short read – is it normal to have 0 coverage in some regions? 0 I recently miniprepped the whole genome of strain of interest and decided to submit the sample for NGS (2 x 150bp) When the .fastq data came back, I trimmed it (trimmomatic), mapped…

Hello everyone! I am a beginner with bioinformatics but at the company I work at we have a genome assembly of one of our crops. I wanted to annotate the genome and to do so I used a piece of python code in ubuntu. I used the Augustus Arabidopsis database…

Classification for low quality variant on IGV 0 Hello, I have a region which is low quality, but I was wondering how I can describe this region – it occurs next to a high coverage block of reads but I am not sure how to describe this. Does anyone have…

Calculate the percentage of genomic region covered from the BED file. 0 Hello, I have multiple exome capture kit bed files. I need to know if there is any method to calculate how much portion/ percentage of the region in a gene, each capture kit covers. Thereby, I can compare…

IGV – is it possible to tell what allele a read is from? 0 Hello, Does anyone know if it is possible to work out which allele a read is referring to in IGV? For example, if I have a heterozygous variant, is it possible to work out which allele…

Bowtie is a versatile and widely used bioinformatics tool for short read alignment and mapping in the field of genomics. It plays a crucial role in the analysis of DNA sequencing data, helping researchers understand genetic variations, gene expression, and other important biological processes. Bowtie’s popularity stems from its high…

Head of Genomics & Bioinformatics Job Description Cellino Biotech, Inc. is an innovation- and value-driven, venture capital-backed biotechnology company that is pioneering a transformative platform to manufacture cell-based therapies. The company was founded by a team of interdisciplinary, entrepreneurial scientists and engineers with expertise in laser physics, biology, software development,…

Head of Genomics & Bioinformatics Job Description Cellino Biotech, Inc. is an innovation- and value-driven, venture capital-backed biotechnology company that is pioneering a transformative platform to manufacture cell-based therapies. The company was founded by a team of interdisciplinary, entrepreneurial scientists and engineers with expertise in laser physics, biology, software development,…

Job Description Overall Position Summary and Objectives Under this task order, the contractor will provide support services to satisfy the overall operational objectives. The primary objective is to provide services and deliverables through bioinformatics support services as part of an existing bioinformatics team. Minimum EducationMaster’s Resume Max Pages15 Certifications &…

Why do I need to sort and index gtf file for IGV? 0 I want to visualize some bam files on IGV. I had aligned my samples to a custom reference through STAR so I am trying to add this to IGV. I added the .fa file easily but I…

Expect heterozygous variant from reads 0 Hello, I have a diploïd yeast genome. There is a gene cassette, inserted in a heterozygous way, confirmed by PCR in this sample. The sample was sequencend by CCS Pacbio technology. I did a diploïd assembly with hifiasm of this sample, which gave me…

. 2023 Jun 29;14:1089956. doi: 10.3389/fgene.2023.1089956. eCollection 2023. Affiliations Expand Affiliations 1 Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy. 2 Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy. Item in Clipboard Chiara Frascarelli et al. Front Genet. 2023. Show details Display…

How to overlay tracks in IGV? 0 I am trying to overlay these four tracks on IGV so that they are color-coded by importance, however the overlay tracks feature isn’t working. When I select Tracks > Overlay Data tracks, a dialogue box pops up saying “overlay tracks by” and the…

How to make Cicero Spider Plot 0 Hello, I have a list of enhancers and the genes they target that looks like this for mm10 genome: Enhancer Target Gene 1: chr4_98727908_98728497 L1td1 2: chr9_78623220_78624062 Cd109 3: chr9_78615332_78616035 Cd109 4: chr2_146299937_146300524 Insm1 5: chr2_146218029_146218779 Insm1 Using this list, I would like…

26All paired-end Illumina libraries were inspected with FastQC v0.11.5() and trimmed and filteredwith Trimmomatic v0.36 (66). Read mapping was performed with sppIDer pipeline(81) using a combined reference including the genome assembly of CBS9595 (asrepresentative of P1 lineage, Supplementary File 1 for more details) and CBS14141(as representative of P2 lineage, Supplementary…

Patients The WGS and clinical data of 235 patients with A-T were provided by the Global A-T Family Data Platform of ATCP. Our access to the data was approved by the Data Access Committee of ATCP. Selected patients with A-T enrolled at the Manton Center for Orphan Disease Research under…

Identifying enhancers that regulate certain genes 0 Hi everyone – I’ve got a list of genes that I am interested in identifying the enhancers that regulate their expression. I’ve got the BED file for the enhancers within my cell line of interest generated by intersecting ChIP-Seq peaks of different histone…

How to add new coordinates to the existing .gtf annotation file 1 I have a few sequences that are not annotated in the reference genome. Using BLAST and STAR I was able to get the coordinates of all those sequences. Using IGV, I could visualize that my transcriptomic data has…

Identify binding motifs within large super enhancer region 1 Hello, From my H3K27ac ChIP seq data, I have identified 500 super enhancer regions using Homer’s findPeaks -style super. From the super enhancer regions, I found 4 enriched binding motifs within the 500 super enhancer regions using Homer’s findMotifsGenome.pl. First, I…

Sorry if this seems ignorant, but that is why one asks questions: to learn. While investigating a WGS sequence within IGV, there appear numerous heterozygous y alleles across the full Y chromosome. How can this occur in general? How common is this? At what point is it not common, i.e….

Optimization of the pipeline on monoclonal and simulated mixed infection samples Towards optimizing GATK4 for P. falciparum, the creation of an improved training “truth set” for the pipeline was key. To filter raw VCFs with a high quality truth callset, which is difficult to obtain using wet laboratory methods, a…

Bioinformatics Scientist We are seeking a highly motivated and skilled Bioinformatics Scientist to join our R&D team. The successful candidate will be integral to our genomics research efforts. This role requires expertise building pipelines from sequencer output to feature generation from both RNA and DNA sources. The candidate should have…

A ggplot2 genome-wide CNV plot? 0 Dear Biostars, I am trying to recreate the following graph depicting human CNV frequency information: My initial data is contained in .bed files and classifies each CNV as a gain or loss. I have been thinking if this is simply performed using ggplot2 and…

Ronca, S. E., Ruff, J. C. & Murray, K. O. A 20-year historical review of west nile virus since its initial emergence in north america: Has west nile virus become a neglected tropical disease?. PLoS Negl. Trop. Dis. 15, 1–20 (2021). Article  Google Scholar  Diaz, A., Coffey, L. L., Burkett-Cadena,…

Visualize methylation status in Pacbio Hifi read 2 I want to know how to visualize methylation status in IGV. I tried to visualize by clicking color alignments by -> base modification (or bisulfite mode -> CG). But It shows only red colors and no blue colors in IGV. Please let…

3′ Single Cell RNA Seq Reads mapping to promoter region of gene 0 Hi! I am trying to visualize my reads from a 3′ Single cell RNA seq run in IGV. I am using the bam file from the cell ranger output. For some reason, I am encountering a lot…

Reads in IGV are mostly in intron regions 0 I was analyzing a published datasets related to Patch-seq: RNAs from soma or dendrites was sequenced. After visualizing the BAM files in IGV, it is weird to see that most of the reads fall into intron regions. I am wondering if…

Bioinformatics is a field that combines biology, computer science, and statistics to analyze and interpret biological data. With the advent of high-throughput sequencing technologies, the amount of genomic data generated has increased exponentially. This has led to the development of bioinformatics tools that can handle large-scale genomic data and provide…

How to discard alignments from SAM/BAM file that have mismatches 0 Hi all, I have sequenced the mRNA of a heterologous library expressed in human cells using nanopore. Then I mapped the reads from the fastq files to the reference database of the library using the minimap. Then I filtered…

Whether they’re in the brain, on the skin, or in the liver, solid tumors are difficult to treat. Because they arise from healthy cells that go haywire, every person’s tumor is different. This tumor heterogeneity means that there is often no “one size fits all” treatment, even for the same…

differential splicing between two groups for 5 genes 1 I have an experimental group where I observed the presence of a handful of genes (5 genes) that I was not expecting to see. To assess the validity, I look at the read alignments on IGV and the read phred scores…

The National Institute of Deafness and Other Communication Disorders, Bethesda, Maryland Position Description: The Division of Intramural Research (DIR), National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Department of Health and Human Services (DHHS) seeks a Staff Scientist. The NIDCD intramural program comprises a highly…

Confirming intron length 1 Hi all, I have RNA-Seq data (ctrl vs kd) and performed a bunch of analyses. One of the analyses I performed was via rMATS tool to find possible retained introns. In the rMATS output, I do get coordinates for individual retained introns but I think depending…

Identify similarly mapped reads in BAM/SAM? 1 I have a BAM (or SAM) file of reads mapped to a reference genome. I would like to identify which reads are mapped similarly/to approximately the same location, which reads might be “orthologs”. For example, when visualizing the BAM file in IGV, the…

Allele design and guide selection For multi-exon genes, a critical region (one or more exons) was identified as shared among all annotated full-length transcripts whose removal was predicted to result in a frame-shift mutation and introduction of premature stop codon greater than 50-nt from the final splice junction increasing the…

Ethics The Australian Genomics Acute Care study has Human Research Ethics Committee approval (HREC/16/MH/251). Parents provided informed consent for participation in the study, following genetic counseling. Study design and participants The Acute Care Genomics program is a national multi-site study delivering ultra-rapid genomic testing to critically ill pediatric patients with…