Tag: IGV

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…

Flaxman JP, Smith DW, Mackenzie JS, Fraser JRE, Bass SP, Hueston L, et al. A comparison of the diseases caused by Ross River virus and Barmah Forest virus. Med J Aust. 1998;169:159–63. Article  Google Scholar  El-Hage CM, Bamford NJ, Gilkerson JR, Lynch SE. Ross River virus infection of horses: appraisal…

I have two bam files from single-cell RNA sequencing mapped to the reference genome using CellRanger, I can view them in IGV and I have a particular region where the pattern of reads mapped to the reference genome are different between the two bam files but when I try the…

We are seeking a remote full-time Bioinformatics Pipeline Engineer who has the skillset to construct and maintain scalable genomic analysis pipelines. Your role will not only be centered around development for pharmacogenomics, cancer, and infectious diseases biosurveillance. We value someone with the expertise to implement Python and shell scripting in…

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 &…

IGV insertions 0 Using CLC I get the following mutation: KEAP1 ENST00000171111:c.254dupA ENSP00000171111:p.Tyr85fs but why is it dupA, although a “T” is inserted!? It should be correct: c.254insT isn´t it!? Or is it because KEAP1 is on the negative strand on chrom. 19 and the igf refers always to the…

Hi all, I am expressing a GFP synonymous variant library in human cells and sequencing its RNA on the nanopore and I am having some trouble analysing the data. Initially, I basecalled all the fast5 files using the super accuracy model in the guppy basecaller, then I discarded the reads…

weird behaviour on bedtools 0 Hi All, I want to extract the counts on defined regions (my.bed). But i’m not able to understand the results. The command says extract the counts form the bam files using bed file also the region of the bed region has to have >=80%. multiBamCov…

I am analyzing PacBio IsoSeq data and I am using StringTie to assemble transcripts. I noticed the difference in the output files when I add a reference genome annotation (-G option in StringTie). In general I have less transcripts assembled when I give as imput reference genome annotation and I…

Annotation of short-read scRNA-seq data with isoform-level information Using fluorescence-activated cell sorting (FACS), we isolated the Lineage-negative, cKit (Cd117) positive (LK) cell fraction of mouse bone marrow cells, a population containing stem and progenitor cells14 from young (8 weeks old, n = 3) and aged (72+ weeks old, n = 3) mice. We generated…

IGV displays genomic coordinates in a 1-based system or 0-based? 0 Could you please help me determine whether the Integrative Genomics Viewer (IGV) displays genomic coordinates in a 1-based or 0-based system? I have been unable to locate a reference page addressing this question. Your assistance would be greatly appreciated….

Sakai AK, Allendorf FW, Holt JS, Lodge DM, Molofsky J, With KA, et al. The population biology of invasive species. Annu Rev Ecol Syst. 2001;32:305–32. Article  Google Scholar  Allendorf FW, Lundquist LL. Introduction: population biology, evolution, and control of invasive species. Conserv Biol. 2003;17:24–30. Article  Google Scholar  Erickson AB. The…

Mutant collection development We mutagenized 2,700 seeds of the wheat–Th. elongatum introgression line RWG34 containing Sr43 (ref. 29). Dry seeds were incubated for 16 h with 200 ml of a 0.8% (w/v) EMS solution with constant shaking on a Roller Mixer (Model SRT1, Stuart Scientific) to ensure maximum homogenous exposure of the…

interpreting inversions on IGV 1 I just started working with PacBio and Nanopore long reads, after some preliminary QCing I mapped the reads using minimap2. I am looking at the inversions for now and I have igv images for one of my regions. I want to know is it how…

Tool:open-cravat: variant annotation tool 3 open-cravat is an open-source platform for rapidly developing, using, and disseminating variant annotation tools. It can handle unlimited number of variants in VCF format input files as well as its own input format and produce tab-separated text output files and excel spreadsheets. It is command-line-based…

I am trying to reproduce an analysis result, and there is a requirement regarding the format of the result: the ‘3’ rule ‘: all mutations should be expressed in a position close to the end of the gene transcription direction (3’ end). The result I obtained is(annotate from VEP) Chromosome…

How to improve signal to noise ratio in sequencing samples? 1 Hi everyone! I’m dealing with NGS data derived from CUT&TAG experiments and I’m quite new to the field. I ended up with very noisy IGV profiles and sample coming from my antibody of interest looks like my IgG one….

 This article explores sequencing coverage fundamentals. Uncover key concepts and discover how highly accurate long-read sequencing provides a comprehensive view of the genome, at any coverage level.  What is sequencing coverage? Genomics professionals use the terms “sequencing coverage” or “sequencing depth” to describe the number of unique sequencing reads that…

Topic participation The examine protocol was accredited by the ethics committees of Osaka College and associated medical establishments in addition to the Translational Well being Science and Know-how Institute (Faridabad). Japanese people (n = 343) for whom intestine metagenome shotgun sequencing had been carried out in earlier research had been included on…

Estimate sizes of repeats in a especific Gene 0 Amateur problem here: We know that it is possible to use the ExpansionHunter tool to estimate sizes of such repeats by performing a targeted search through a BAM/CRAM file for reads that span, flank, and are fully contained in each repeat….

IGV custom tracks from gff3 files; how to customize feature blocks “shape”? 1 Hi, In IGV, I am using gff3 files to visualize the genomic location of features that I identified through my experiments. The features are visualized as rectangular “boxes” with strand direction shown as arrow heads. I would…

Subject participation The study protocol was approved by the ethics committees of Osaka University and related medical institutions as well as the Translational Health Science and Technology Institute (Faridabad). Japanese individuals (n = 343) for whom gut metagenome shotgun sequencing were performed in previous studies were included in this study46,47,48. Among these…

How to extract regions from BAM file on remote server and visualize long-read alignments in IGV? 1 Hello, I have code that indicates there are a number of SNP mutations at specific locations for different cell types and none for others. I need to align all the respective longreads at…

how to input bedpe file in IGV 0 Hello, I have a bedpe file with interacting region and its interacting score. I want to view this bedpe file in IGV. But its showing error when inputing. The file (bedpe) look like this: When I input the file in IGV: File>…

Patients cohort Among consecutive patients who underwent BRCA tumour testing through ION Torrent-based sequencing between August 2017 and February 2022, we retrospectively selected 222 high-grade ovarian cancer (HGOC) patients with the following histological subtypes: 203 serous (HGSOC), seven endometrioid, five clear-cell and seven with mixed histotypes. Since NGS BRCA1/2 tumour…

How to interpret plot from igv_session.xml file 1 Hi all, I want to check if a gene is of interest in the open chromatin region so after typing its name, I got this plot with peaks. So do peaks mean open chromatin region? And if we have no peak mean…

After trimming the sequence data obtained in this study based on strict criteria, more than 95% of all read pairs were mapped to the Gallus reference genome, although some variation in depth was observed. Thus, the assembled sequence data were considered high quality. In addition, the detection of junglefowl ERV-LTRs…

BAM files from RNAseq showing counts in genomic regions with no genes present 0 I am trying to see if whole transcriptome sequencing has good coverage for miRNA as well. when I load BAM files from one of the samples, and look for miRNA, I can see that there are…

Hello, I’m currently following this paper Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. It is a ChIP-Seq to generate genome-wide maps of 34 chromatin modifications (17 acetylation marks, and 17 methylation marks) and the histone variant H2AZ. B cells were either naïve (G0) or activated for…

The thinkness indicates whether something is an intron, a coding exon or a UTR. The very thin lines are introns, the full thickness boxes are coding exons and the thinner boxes are UTRs. UTRs, untranslated regions, are exons, they are included in the final mRNA, but they don’t code for…

kallisto pseudoaligned bam files to IGV 2 Hi, has anyone found the solution for this? I am running kallisto with –genomebam option along with the –chromosomes, The bam file generated is already sorted by kallisto and indexed so I think I do not have to sort it again. I uploaded…

OCT4 alone was insufficient to reprogram PBMCs into iMSCs directly Previously, we reported that lentivirally expressed OCT4 could directly reprogram human cord blood CD34+ hematopoietic progenitor cells into iMSCs with very high efficiency11. Therefore, we first tried to convert human PBMCs into iMSCs by overexpressing OCT4 alone using a clinically…

Abstract We present Genomics to Notebook (g2nb), an environment that combines the JupyterLab notebook system with widely-used bioinformatics platforms. Galaxy, GenePattern, and the JavaScript versions of IGV and Cytoscape are currently available within g2nb. The analyses and visualizations within those platforms are presented as cells in a notebook, making thousands…

Hi everyone, I am trying to see chromosome coordinates (.bed file) are in a gene in the same direction, opposite direction, or not overlapping a gene. I downloaded the genome file from biomart. Here is the command for i in *_sorted_removed.bed; bedtools intersect -wa -S -a $i -b biomart_mm39.bed >…

How to force bcftools to call all variants 1 Hello I am using bcftools to call variants with this command: bcftools mpileup -Ou -b bamlist -f ref.fasta | bcftools call -Ob -mv >variant.bcf However, for some specific variants that I know to exist (looking at bam files with IGV), I…

I’m looking for help understanding the example of spanning alleles and multi-allelic loci on luntergroup.github.io/octopus/docs/guides/advanced/vcf/ The ALT field values are OK, but the GT values don’t make sense to me. BAM files in IGV-style display show 3 samples. 1st, HG002, has a 4-bp del starting at 728 in half the…

Confused on strandedness, what are antisense transcripts? 1 Hello, I am trying to wrap my head around anti-sense transcripts. When looking at refseq’s annotations on IGV you can see a (-) or a (+) for each transcript. From reading this paper www.ncbi.nlm.nih.gov/pmc/articles/PMC3664467/#sec-2title I understand that transcription from the antisense strand…

Gaia CNV error TCGA data 0 Dear All, I am trying to analyze some TCGA CNV data using the GAIA package. I followed the tutorial from @kevinblighe. Everything runs well and at the end, the error below come up. Has someone witnessed this before anc could some one propose a…

how to get to a VCF from bam files 0 Hello, My situation is as follows: I have two groups of reads/Individuals that differ in terms of indels (one group has the indels, the other doesn’t). I already Mapped them and generated bam files. So, now I am struggling to…

First, you can read the newsletters available. We also invite you to watch our training slides (Linux, Cluster) for SLURM cluster. Then, if you did not find what you are looking for, you can use the form to contact us….

Obtain number of base pairs in a genome 1 HI! It’s going to be a stupid question since I’m not anyhow related to bioinformatics – I’m interested into how can I obtain the number of base pairs in my genome sample. I’m trying to remake the experiment that was made…

I generated summit.bed files from my experiment cut&run, and I followed the below steps to get and visualize the bigwig files. 1) I used awk to get a bedgraph: awk ‘{printf “%s\t%d\t%d\t%2.3f\n” , $1,$2,$3,$5}’ myBed.bed > myFile.bedgraph 2) Sorting the bed files: sort -k1,1 -k2,2n myFile.bedgraph > myFile_sorted.bedgraph 3) Chrom.size:…

HTseq no features 0 I have got some problem when analyzing my RNAseq data and I would like to seek for a help. Here is the brief description of my pipeline: Obtained fasta file of 150 PE reads from Novaseq platform followed by non-stranded library prep I conducted fastQC and…

How does 10x Genomics 3′ single cell data have reads aligning to exons that aren’t terminal? 1 I have 10x single cell data from a 3′ expression kit. From what I understand the poly(dT)VN captures the end of the transcript. We sequenced 150 bp. I am now visualizing my BAM…

VCF file filter for breakpoints 0 Hi, I am trying to filter VCF file and extract breakpoints. Does anyone know how to do it using bcftools? I have extracted SV calls using sniffles with the BAM file I had after long read sequencing. Now I would like to use bcftools…

what does total count mean at a location in IGV 0 Hi All, In a BAM file when loaded in IGV and then when clicked on a location (eg: 27792) it shows that the Total reads at that location is 27 and DEL 215. But in that location it can…

Very high coverage Nanopore alignment Hg38 0 Hi, I aligned my first Nanopore reads on the hg38 reference. Then, I used bedtools genomecov to get an idea about the mean coverage over the genome. I noticed some bases have a very high coverage >20,000X , whereas the mean coverage is…

Need help with IGV interpretation 0 Hello all, I wanted to confirm if this is a true deletion? based on what i can observe, there is a drop in coverage, and it is also supported by the red line within the reads. However, i am concerned if 1 read is…

Hi! I am trying to run the Gatk HaplotypeCaller (human data): ./gatk-4.1.2.0/gatk HaplotypeCaller\ –reference ref.fa \ –input file.bam \ –genotyping-mode GENOTYPE_GIVEN_ALLELES \ –alleles allele_chunk_file.vcf \ –intervals file.bed \ –output out/file.vcf After running the above command for any given sample, only ~ 3 sites are called and all of them have…

bamComparing ChIp-Seq samples with strange coverage between chipped and Input 0 I’m having some troubles both estimating the quality and understanding the results of my ChIp-Seq samples as well as to decide how to continue. I hope I can find some help/advice here. I have three conditions, each with duplicates…

Principal Bioinformatics Engineer Form Bio is working with Colossal Biosciences to build the future of genome engineering, and that requires new tools, and we’re looking for someone who is interested in breaking ground on projects across our species teams. The Principal Bioinformatics Engineer needs to have strong programming skills, a…

Calling zero mapping quality variant 0 Hello Is it possible to call variant with read that has zero mapping quality at the region? I found that there is INDEL in my BAM file when I visualize in IGV but the variant is not in gVCF, I have checked the average…

Genome data visualization 0 Hi, Please I need help with producing visualization for genomic DNA regions such as seen in these figures I obtained from a publication: The other image also shows the regions of a chromosome by color. I just need information on the right tools (not IGV) that…

An ENU-induced mutagenesis screening for genes involved in mouse vocalization To identify novel genes involved in mouse vocalization, we set up an ENU-induced mutagenesis screening (Fig. 1a). To this end, we crossed ENU-treated G0 males with untreated C57BL/6 J females, and through the use of an USV detector, identified G1 pups with…

How I know the genome assembly quality by the low coverage Pacbio data ? 0 Hi, I have finished the assembly genome, and i have a low average Pacbio data. I want to estimate the quality of the result. So, i map the Pacbio data to the aseembly genome by…

IGV resizing tracks 1 Is there a way to resize a collection of bam tracks in IGV so that they all take the same height? Say, there are 20 bam tracks loaded from an idxsession file, and corresponding coverage tracks open, how can they be made the same height so…

CHICAGO – A group at Spain’s National Center for Genomic Analysis-Center for Genomic Regulation (CNAG-CRG) in Barcelona has harnessed a protocol for accessing sequencing and variant data to help assess potentially pathogenic genetic variants within the context of a European Union-funded program to improve diagnosis of rare diseases. The CNAG-CRG…

Job Posting for Scientist II, Bioinformatics at PTC Therapeutics, Inc. Job Description Summary: The Scientist II, Bioinformatics is responsible for planning and performing scientific experiments that contribute to PTC’s research and drug discovery activities. The Scientist II is also responsible for communicating experimental results to his/her supervisor and…

Detection T cell receptor transcripts 2 Hello, I planned to explore diverse T cell receptor transcripts using long-read sequencing. So I transfected TCR mini gene into cells and got sequencing data. I mapped my data to genome reference and visualize it via IGV. But I couldn’t see any transcripts from…

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…

Bioinformatics Alignment/Map (BAM) is a powerful tool used to analyze and compare biological sequences. BAM is used to identify genetic variations, detect structural rearrangements, and compare different genomes. It is an essential tool for many areas of bioinformatics, including genomics, proteomics, and transcriptomics. In this article, we will discuss 10…

ChIP-seq problem 0 Hello, I have just uploaded two bw files to IGV, they are from the same experiment, only the second one was sequenced more. When I load them more I notice that the file sequenced more has peaks that are lower, why is that in your opinion? N.B….

Any good tools for biological annotation of ChIP-seq broadpeak (H3K9me3, H3K27me3)? 0 Hi, I have called ChIP-seq broadpeak (H3K9me3, H3K27me3) using SICER2 in mm10. The peak looks good and consistent with the IGV findings. Is there any good tools to annotate these broad peaks to coding genes? I know GREAT(great.stanford.edu/public/html/)…

TDF to bed graph — IGV on command line 0 Hi all, I’m trying to convert some TDF files to bedgraph files so that I can do a genomic leftover on them (as far as I can tell, I can’t lift over TDF files). This google group answer here (groups.google.com/g/igv-help/c/RcZw5YB5SOQ)…

Description The Genome Bioinformatics Analyst works independently to curate disease, gene and variant knowledge including variant interpretation, reporting and consultation with laboratory staff, physicians and genetic counselors. The analyst participates in clinical test development, validation and maintenance of data analysis pipelines, monitoring of quality metrics and the analysis of large…

How to check gene properties (eg GC, repetitiveness, average expression level)? 0 Hello, I am trying to compare the data from 2 sequencing machines. I aligned my data with Kallisto and then I performed DESeq2 like I normally do. I was checking to see if I was getting similar results…

Samtools Convert Sam To Bam With Code Examples In this session, we’ll try our hand at solving the Samtools Convert Sam To Bam puzzle by using the computer language. The code that follows serves to illustrate this point. # Basic syntax: samtools view -S -b sam_file.sam > bam_file.bam # Where:…

What sequencing/alignment artifact is this? 0 I’m calling mitochondria variants with mutect2 and one variant looks like an artifact but I don’t understand what could be the cause. It looks like from IGV (picture below) that this variant is always at the same position on forward and backward reads. Also…

Bedtools Bam To Bed With Code Examples With this article, we’ll look at some examples of how to address the Bedtools Bam To Bed problem . bedtools bamtobed [OPTIONS] -i <BAM> As we have seen, a large number of examples were utilised in order to solve the Bedtools Bam To…

Hi everyone, I am currently working on a medium-sized WES cohort study and wanted to know what the bioinformatics community would regard a cutting-edge workflow. As the big labs usually utilize GATK I also started with that. The results for SNPs are ok, but manual inspection (IGV) still uncovers a…

Vacancy title: Principal Biostistician/Bioinformatics [ Type: FULL TIME , Industry: Research , Category: Research ] Jobs at: Kenya Medical Research – KEMRI Deadline of this Job: 06 October 2022   Duty Station: Within Kenya , Kisumu , East Africa SummaryDate Posted: Tuesday, September 20, 2022 , Base Salary: Not Disclosed…

Description Purpose:The scientist works independently using a robust math toolbox to discover solutions for a diverse portfolio of interesting and challenging problems. The scientist develops, implements, and monitors advanced analytic, medical informatics, and predictive modeling tools for health care programs at the UPMC. The scientist normally works Monday through Friday…

Understanding bam tracks 0 Sorry i am having trouble understanding this concept. For example, when I view a bam file after alignment in igv, I see that there are different tracks that form. How are these tracks formed/why do some aligned sequences belong together or are part of the same…

Patients and controls The patient 1 was 38 years old and consulted for infertility after he and his partner had been trying to conceive for 2 years. The patient was the first child of unrelated parents, and he had four brothers and five sisters whose fertility status could not be determined…

Issue Title State Comments Created Date Updated Date Mapping reads against multi references. Any proposition? open 0 2022-06-28 2022-06-30 Inversion between tandem repeats yields misalignment closed 1 2022-06-21 2022-06-30 use minimap2 to extract mitochondrial reads from genome assembly open 0 2022-06-20 2022-06-30 Asking for #301 to be reopened closed 0…

DNM filtering in 100,000 Genomes Project We analysed DNMs called in 13,949 parent–offspring trios from 12,609 families from the rare disease programme of the 100,000 Genomes Project. The rare disease cohort includes individuals with a wide array of diseases, including neurodevelopmental disorders, cardiovascular disorders, renal and urinary tract disorders, ophthalmological…

I received (from manufacturer) several .bam files and I used four callers (samtools, freebayes, haplotypecaller, deepvariant) to find some sequence variants. In obtained .vcf files, I took a closer look to some calls. I found interesting, homozygous one rs477033 (C/G Ref/Alt) with flag ‘COMMON=0’ and very low MAF. I also…

Hi everyone, first time working with mouse samples and unfortunately, there are fewer resources available for the latest mouse Ensembl genome than I was expecting. What I’ve done: I performed rRNA depletion on total RNA extracted from mouse tissue and created Illumina libraries using a cDNA synthesis kit with random…

Does anyone know how to get the headers for a bam.tdf file converted to a bedgraph file? 0 I followed this thread: Conversion from tdf to bed format Converted like this: igvtools tdftobedgraph file.tdf file.bedgraph Now I have a bedgraph without headers but I have no idea what the last…

Introduction Primary testicular diffuse large B-cell lymphoma (PT-DLBCL) is a rare and aggressive form of mature B-cell lymphoma.1–3 PT-DLBCL was the most common type of testicular tumor in men aged over 60 and characterized by painless uni- or bilateral testicular masses with infrequent constitutional symptoms.4–6 PT-DLBCL shows significant extranodal tropism,…

INTRODUCTION Mammalian life starts with the fusion of two terminally differentiated gametes, sperm and oocyte, resulting in a totipotent zygote. After going through preimplantation development, the zygote reaches blastocyst before implantation. The two most important events taking place during preimplantation development are zygotic genome activation (ZGA) and the first cell…

I am implementing a website in Python with Django framework and using django-plotly-dash to display data. I am trying to use dash_bio’s IGV feature to display some chromosome data, but when I attempt to call the functionality, I receive the following errors and the callback that returns ‘dashbio.igv’ is unable…

bcftools merged vcf file assigns all variants to one sample 0 I’ve made one vcf file for each of three samples. I then combined them using bcftools, like so: # Make a list of vcf files to merge cat “${OUT}/results/variants/vcf_list” /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/3a7a-10.vcf.gz /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/MF3.vcf.gz /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/R507H-FB_S355_L001.vcf.gz Then merge the list: bcftools merge -l…

Hi all, We store our alignment files on aws s3. I would like to be able to open them with IGV without needing to download them completely, but I can’t find an optimal solution. If I get a pre-signed url it works but it’s not convenient. I try to follow…

Materials and Methods Genomic data was collected as part of the MDS National History Study or The Cancer Genome Atlas project and consented appropriately under those protocols 8 Sekeres M.A. Gore S.D. Stablein D.M. DiFronzo N. Abel G.A. DeZern A.E. Troy J.D. Rollison D.E. Thomas J.W. Waclawiw M.A. Liu J.J….

doi: 10.1007/s00414-021-02763-0. Online ahead of print. Affiliations Expand Affiliations 1 Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan. hnakani@juntendo.ac.jp. 2 Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan. 3 Department of Forensic Medicine, Juntendo University School of Medicine,…

Clinical Bioinformatics Analyst (m/w/d) PENZBERG, GERMANY Foundation Medicine is leading a transformation in cancer care, where each patient’s treatment is informed by a deep understanding of the molecular changes that contribute to their disease. As a molecular information company, we are focused on fundamentally changing the way in which patients…

**Description** UPMC Presbyterian is hiring a Genome Bioinformatics Analyst to join the Molecular and Genomic Pathology Laboratory (MGP) team! This role will work a daylight schedule Monday through Friday. No weekends or holidays are required! The Molecular and Genomic Pathology Laboratory (MGP) is a dynamic state-of-the-art clinical laboratory that prides…

Create junctions from Bed file for IGV visualization 0 Any advice for creating junctions file from a bed-like file? My bed file looks like this: chr start end chr star end I have tried to copy the format used in TopHat (junctions file). But I can’t see the junctions in…

Hi everyone! I have a query regarding variant calling from a high coverage site on the basis of the maximum likelihood variant. I have RNA-seq data mapped bam file. I called variant using the below command. “bcftools mpileup –max-depth 10000 -Oz -f ref.fa sample.bam | bcftools call -mv -Oz -o…

Forum:2021: state and usuge of compressed file standards better than BAM and FASTQ 3 Extra compressed formats for raw/aligned reads and variant tables have been around for some time but I think saw slow adoption. Our current disk space usage is making us have another look at switching to file…

The BAM files can be opened remotely (ftp, http) or locally (local). The index file must be found in the same directory as the BAM file in order to view it. The index should be named by appending “. The file name is changed from “bai” to “bam”. How Do…

Hi, I have a problem processing ChiP-Seq data. I have two datasets of H3K9me3 replicates aligned to the reference genome mm39. For peak calling, I used hiddenDomains. About my problem: replicate A shows peaks on all chromosomes after peak calling, replicate C shows no peaks on Chr12. The .bw files…

IDI seeks to hire a Bioinformatics Scientist (BS) for the centre. The BS will be a fulltime staff who is familiar with the application of computational and biotechnology capabilities to biomedical and public health problems like genetics, clinical and medical research, as well as other data intensive analyses. By coordinating…

Cnv Visualization 4 I’ve produced a list of CNV(copy number variation) data like below: chr10 10271614 10659796 DEL chr10 107242905 107243436 DEL chr10 107940570 107941687 DEL chr10 108020235 108022638 DEL chr10 111562017 111568300 DEL chr10 116956782 117389734 DEL chr10 117005207 117396827 DEL Just wondering if we have any VISUALIZATION software…

Quick question about IGV 1 Hi, I’m using IGV to check variant. I saw this plus and minus at yellow highlight. What is the meaning of +, – ? Pair? Thank you. IGV • 128 views I would think that it indicates the direction of a read for the variant,…

Pile up reads without reference? 1 Hi everyone, I have multiple groups of reads (count < 1000) which derived from a number of novel junctions, with each reads contain minimum ~10bp overhang on the other side (i.e., exon). Because the number of random links between exon-exon can be quite large…

How do I run IGV on the sever 1 I use putty to connected to the sever, I already use wget and unzip to have IGV and Java11 download on my sever, and add them in the environment variables by edit bashrc file. But when I try to run IGV,…