Tag: IGV

Any good tools for biological annotation of ChIP-seq broadpeak (H3K9me3, H3K27me3)?

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/)…

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TDF to bed graph — IGV on command line

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)…

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Genome Bioinformatics Analyst at UPMC

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…

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How to check gene properties (eg GC, repetitiveness, average expression level)?

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…

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Samtools Convert Sam To Bam With Code Examples

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:…

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What sequencing/alignment artifact is this?

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…

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Bedtools Bam To Bed With Code Examples

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…

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GATK vs DeepVariant : bioinformatics

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…

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Job – Principal Biostistician/Bioinformatics job at Kenya Medical Research

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…

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Bioinformatics Scientist in Pittsburgh, PA

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…

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Understanding bam tracks

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…

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iPSCs derived from infertile men carrying complex genetic abnormalities can generate primordial germ-like cells

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…

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Lh3 Minimap2 Issues

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…

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Genetic and chemotherapeutic influences on germline hypermutation

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…

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snp – Reference variant detected as altered one in bam file

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…

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Low transcript quantification with Salmon using GRCm39 annotations

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…

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Does anyone know how to get the headers for a bam.tdf file converted to a bedgraph file?

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…

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BTG2 gene predicts poor outcome in PT-DLBCL

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,…

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Profiling and functional characterization of maternal mRNA translation during mouse maternal-to-zygotic transition

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…

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python – How can I fix the dash bio error: devtools cannot load source map dashbio@1.0.1 bundle.js.map?

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…

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bcftools merged vcf file assigns all variants to one sample

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…

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Read bam/cram file with IGV from aws s3

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…

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Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence

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….

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Estimating individual mtDNA haplotypes in mixed DNA samples by combining MinION and MiSeq

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,…

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Clinical Bioinformatics Analyst (m/w/d) – Foundation Medicine GmbH – Biology & Life Sciences

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…

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Genome Bioinformatics Analyst – Pittsburgh

**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…

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Create junctions from Bed file for IGV visualization

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…

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How to call variant by –max-depth for RNAseq

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…

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state and usuge of compressed file standards better than BAM and FASTQ

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…

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How To Open Bam Files Without Software?

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…

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Problem with peak calling using hiddenDomains: entire chr12 lacking peaks.

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…

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Bioinformatics Scientist at Infectious Disease Institute

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…

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Cnv Visualization

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…

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Quick question about IGV

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,…

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Pile up reads without reference?

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…

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How do I run IGV on the sever

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,…

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samtools – How to analyze IGV alignment

I’m working on a project where I am analyzing the performance of an alignment workflow. My goal is to find regions in the resulting BAM file where there are outstanding discrepancies or anything that indicates my assembly/alignment has “mistakes”. My workflow so far: input paired end FASTQ files (human) into…

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How can I know what is a good and bad variant call?

How can I know what is a good and bad variant call? 0 Hi, this is my first post/question, sorry if it is not allowed. I am generating variant calls with a variant caller. The variant caller I am using is bcftools. I am analyzing/looking the VCF in Excel and…

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Frontiers | Accelerating Complete Phytoplasma Genome Assembly by Immunoprecipitation-Based Enrichment and MinION-Based DNA Sequencing for Comparative Analyses

Introduction Phytoplasmas are wall-less bacterial pathogens that are known to infect numerous plant species and lead to significant agricultural losses (Gurr et al., 2016; Kumari et al., 2019; Pierro et al., 2019). They are parasitic bacteria multiplying exclusively in phloem sieve elements and are transmitted between plants by phloem-feeding insects…

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The provided VCF file is malformed

htsjdk.tribble.TribbleException: The provided VCF file is malformed 1 I have VCF files that I want to convert to a more readable TSV file using GATK VariantsToTable, and I also want to load in the VCF in IGV. However, when trying to do this, I get the same error for both…

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Reads detected/”spill over” on introns after using bamCoverage function from deepTools

Reads detected/”spill over” on introns after using bamCoverage function from deepTools 0 Hello! We recently used the recent version of bamCoverage from the deepTools suite for our ribo-seq and RNA-seq bam files to generate bigwig files. The conversions ran smoothly, however when we loaded the bigwig files into IGV, we…

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Stable lariats bearing a snoRNA (slb-snoRNA) in eukaryotic cells: A level of regulation for guide RNAs

Significance Small nucleolar (sno)RNAs generally guide ribosomal RNA and small nuclear RNA modifications, essential events for ribosome and spliceosome biogenesis and function. Most are processed in the nucleus from lariat intronic RNAs, which are unstable byproducts of splicing. We report here that some snoRNAs are encoded within unusually stable lariats….

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Bioinformatics Scientist – Job at DAWSON in Bethesda, MD

Bioinformatics Scientist Full Time Prof-Entry Bethesda, MD, US DAWSON is a Native Hawaiian Organization 8(a) small business that brings the Spirit of Aloha to our employees. As part of the DAWSON “Ohana”, you will be provided a best-in-class benefits program that strives to ensure our great people have peace of…

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Genome Browser suggestions

Genome Browser suggestions 6 Hi all, I am in search of a Genome Browser that could suit my needs. I already used many times GBrowse, IGV and Jbrowse. GBrowse is too tedious to work with given the way you have to add tracks and given that is very slow when…

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Providence hiring Bioinformatics Scientist 1 in Portland, Oregon, United States

DescriptionProvidence is calling a Bioinformatics Scientist 1 to the Molecular Genomics Lab at Providence Office Park i n Portland, OR. This is a full-time (1.0 FTE), day shift position. This position is a hybrid role between working in the lab and working from home.Apply today! Applicants that meet qualifications will…

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Visualization tools for split read / structural variants

Visualization tools for split read / structural variants 0 Hi everyone, I have been trying to curate my SV call set by visually going through the bamsnap images (a static version of IGV) of each SV region. However, it is difficult to look at long-range information, such as the paired-end…

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Extracting specific regions from bam file as FASTA format

Extracting specific regions from bam file as FASTA format 0 Hello, first time asking, so sorry in advance for beginner’s mistakes. I have an indexed bam file, and I want to extract the FASTA format of all the reads that appear within the defined region (or partially appear) for example:…

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Reads per UMI from 10X Chromium RNAseq runs

Reads per UMI from 10X Chromium RNAseq runs 0 I am working on a set of Drosophila samples sequenced using 10X Chromium pipeline and I need to visualize the reads of individual cells on IGV. Unlike SMARTseq methods which yield an individual BAM file for each UMI, CellRanger outputs only…

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Shaping modern human skull through epigenetic, transcriptional and post-transcriptional regulation of the RUNX2 master bone gene

Study of RUNX2 locus in modern and ancient humans The sequences of the RUNX2 locus (Chr6:45,318,000–45,670,000 hg38, for a total of 352.000 bases) have been aligned in AMH and ancient species’ (Neandertal and Denisovan) genomes to map the changes occurred during recent evolution. We have identified 459 and 470 changes…

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samtools view extract from .bed list to .bam file

samtools view extract from .bed list to .bam file 0 Hi – I am attempting to extract certain regions from a large .bam file into a smaller subsetted .bam file using samtools view. I’m doing so in order to have a smaller file to down/upload for viewing in IGV. I…

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Index genome not working in Tracy

I’m trying to follow the variant calling guide for Tracy. www.gear-genomics.com/docs/tracy/cli/#variant-calling I have a viral genome just as a fasta file, and when I try to call variants like this: tracy decompose -v -a cmv -r CMVrefGenome.fasta -o oututfile inputfile.ab1 It tells me the genome needs to be shorter than…

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How to convert a bcf file to vcf with bcftools?

How to convert a bcf file to vcf with bcftools? 1 I’ve been following the guide on the Tracy website for looking at variants in some Sanger sequences I have: www.gear-genomics.com/docs/tracy/cli/#variant-calling I’ve now generated the bcf files, and it says I can convert these to vcf using bcftools. How do…

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Junior Bioinformatician at the Lymphoma Genomic Laboratory

Junior Bioinformatician at the Lymphoma Genomic Laboratory Open position Junior Bioinformatician at the Lymphoma Genomic Laboratory Institute of Oncology Research (IOR) Bellinzona, Switzerland www.ior.usi.ch www.ior.usi.ch The Institute of Oncology Research (IOR) in Bellinzona, Switzerland, is a rapidly evolving,leading center for basic and translational research in oncology in Europe.IOR is affiliated…

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StringTie creates .tsv value that has null values for every gene id

Isoform Analysis: StringTie creates .tsv value that has null values for every gene id 0 Hi everyone, I am new to bioinformatics and Biostars as a whole. I am doing isoform analysis on some samples and I’ve come across a problem. The following code is what I used for StringTie….

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Bioinformatics Scientist with Security Clearance job in Bethesda at Dawson

Company Description Dawson is a Staffing & Recruiting agency that was founded in 1946 and headquartered in Columbus, OH. They have the vision to help the small as well as large corporations and businesses to recruit the talent that can help them to provide the best customer service with exceptional…

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featureCounts has low successfully assigned reads

featureCounts has low successfully assigned reads 1 After finishing STAR two-step alignment, I got 62% uniquely mapped reads. But featureCounts gives me only 17% successfully aligned rate. featureCounts -T 8 -F GTF -p –countReadPairs -t exon -g gene_id -a ~/genome_ref/gencode.v38.annotation.gtf -o ~/expression/all_counts.txt *.bam I also have a look at other…

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How to load genome on IGV?

How to load genome on IGV? 1 I’m new to IGV and I’m trying to load my own genome but it just isn’t working. This is the genome I’m interested in: www.ncbi.nlm.nih.gov/genome/5296?genome_assembly_id=700425 On the graphical viewer I’ve clicked “Download”, then downloaded the FASTA of the whole thing. The file is…

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FASTQ to VCF pipeline question

FASTQ to VCF pipeline question 0 Hello all, I am new with programming within bioinformatics and long story short, I’m practicing writing pipeline scripts starting with the fastq to VCF pipeline. I am basically at the point where I went from fastq to sorted-bam files, and as I went to…

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How to call variant minimum 3 read coverage to make consensus?

How to call variant minimum 3 read coverage to make consensus? 0 I have a query regarding consensus sequence assembly where reference bases are replaced with variants with a minimum of 3 read depths, using bcftools using the below command. bcftools mpileup -f ref.fasta mapped.bam | bcftools call -c |…

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What is bigwig file?

Asked by: Vada Ratke Score: 4.7/5 (25 votes) BigWig is a file format for display of dense, continuous data in a genome browser track, created by conversion from Wiggle (WIG) format. BigWig format is described at the UCSC Genome Bioinformatics web site, and the Broad Institute file format guide provides…

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bowtie2 mapping qualities of 0

bowtie2 mapping qualities of 0 0 I have used bowtie2 to map paired-end reads together with unpaired reads to a reference genome (default parameters). I noticed when looking at my alignment in IGV, that at some locations there are a lot of reads with a mapping quality of 0. I…

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kallisto genomebam error

Hello! I am trying to produce bam files to load to igv after kallisto quant with –genobam option. This is the code that I am using kallisto quant -i Homo_sapiens.GRCh38.cdna.all.release-100.idx -o $FOLDER -t 12 –genomebam -g Homo_sapiens.GRCh38.100.gtf.gz -c hg38.chrom.sizes_clean_tab.txt –rf-stranded ${FILES[$i]} ${FILES[$i+1]} My chromosome file looks like that, tabbed and…

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Can there be a lot of misalignment with a 150bp paired-ended reading frame?

Can there be a lot of misalignment with a 150bp paired-ended reading frame? 0 For example, is it possible to have sequences displayed on IGV at a position in the genome that is wrong? Is this common? sequencing • 21 views • link updated 40 minutes ago by GenoMax 107k…

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kallisto genomebam not showing reads on igv

Hello! I am trying to produce bam files to load to igv after kallisto quant with –genobam option. After producing and loading the pseudoalignment bam to the igv, it is empty. This is my initial command: kallisto quant -i Homo_sapiens.GRCh38.cdna.all.release-100.idx -o pseudo -t 10 –genomebam -g Homo_sapiens.GRCh38.100.gtf -c hg38.chrom.sizes R1.fastq.gz.trim_1.fq.gz…

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Comparative cellular analysis of motor cortex in human, marmoset and mouse

Statistics and reproducibility For multiplex fluorescent in situ hybridization (FISH) and immunofluorescence staining experiments, each ISH probe combination was repeated with similar results on at least two separate individuals per species, and on at least two sections per individual. The experiments were not randomized and the investigators were not blinded…

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variants only found on inversion reads in IGV

Forum:variants only found on inversion reads in IGV 0 Hi, I used GATK germline variant calling pipeline to call short variants on paired end fastq files. After got the final analysis ready vcf, applied some extra filters, I inspected bam files in IGV for those variants of interest and found…

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IGV deletion insert size

IGV deletion insert size 0 Hi, I am trying to extract variant reads for deletion (large SVs) from DNA-seq bam files. In IGV, variant reads for deletions are labelled in red (insert size larger than expected): IGV link. I am currently using the pysam package to parse bam files. I…

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install biopython jupyter

like BLAST, ClustalW, FASTA, GenBank, PubMed ExPASy, SwissProt, and many more. conda install-c conda-forge ipyleaflet With pip: pip install ipyleaflet If you are using the classic Jupyter Notebook >> import Bio >>> Bio.__version__. For Windows we provide click-and-run installers. The easiest way to install statsmodels is to install it as…

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ATAC-seq sample normalization

What you describe seems to be a difference in signal-to-noise ratio which is not uncommon. This is where more elaborate normalization methods such as TMM from edgeR or RLE from DESeq2 come into play. See the following links on why these methods are superior. The videos talk about RNA-seq but…

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Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols

Forum:Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols 2 Published in the RNA Journal in 2020 – this paper argues that if the original RNA amount in the different samples is different, TPM should not be used to find differentially expressed genes. www.ncbi.nlm.nih.gov/pmc/articles/PMC7373998/ Seems like…

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Is GTA a stop codon ?

Is GTA a stop codon ? 1 I can’t find the stop codons on IVG I know only three: TGA; TAG; TAA IGV • 75 views That’s not a stop codon, that sequence is intron; its not in the transcript at all. Login before adding your answer. Read more here:…

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Functional succinate dehydrogenase deficiency is a common adverse feature of clear cell renal cancer

Clear cell renal cell carcinoma (ccRCC) is by far the most common type of kidney cancer, accounting for ∼80% of all kidney cancers (1). Despite recent advances, metastatic ccRCC is a generally incurable malignancy, with a 5-y survival rate <20%, highlighting the need for further biologic and therapeutic insights in…

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Problem with viewing BAM files in IGV

Problem with viewing BAM files in IGV 1 Hi everyone, I’m quite new to bioinformatics and I’m having some beginner problems with IGV. I’ve got some BAM files that were generated using the GATK best practice pipeline for SNP discovery, with BAI files located in the same directory. I’m using…

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difference between treat_pileup and bdgcmp fold enrichment tracks macs2

difference between treat_pileup and bdgcmp fold enrichment tracks macs2 0 Hello, I created bigwig file from a treat_pileup.bdg file generated by macs2 and also used treat_pileup.bdg and control_lambda.bdg with macs2 bdgcmp. Here is my codes; macs2 callpeak -t sample.bam -c sample_input.bam -g hs -f BAM -q 0.001 –bdg –outdir /folder…

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The Biostar Herald for Tuesday, September 14, 2021

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…

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ZhaozzReal/SNV_IPA: Detect SNV-associated intronic polyadenylation events from standard RNAseq data

Description Somatic single nucleotide variants (SNVs) in cancer genome affect gene expression through various mechanisms depending on their genomic location. In this study, we found that somatic SNVs near splice site are associated with abnormal intronic polyadenylation (IPA) . Here we give examples to show how to detect SNV-associated IPA…

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RNAseq data mapping mostly to intergenic regions

RNAseq data mapping mostly to intergenic regions 1 Hi everyone, I am working on a project trying to do RNAseq on highly degraded formalin-fixed brain tissues. We extracted RNA using Qiagen FFPE RNeasy kit and the sequencing company suggested to do rRNA depletion method to prepare libraries. We sequenced with…

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How to load user-defined genome in IGV-webapp

How to load user-defined genome in IGV-webapp 0 I would like to create a session in IGV-webapp using a HTML file. The following works with pre-defined genomes (g.e. genome: “hg38”), but I would like to load my own genome. Is there a way to achieve this? <!DOCTYPE html> <html lang=”en”>…

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Sudden coverage increase in IGV

Sudden coverage increase in IGV 0 Hello, I was wondering if anyone knows how to interpret this sudden change in coverage in IGV? I’ve aligned illumin reads of the system against the pacbio generated genome. In the vast majority of this genome, the coverage from one base to the next…

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Pacific Biosciences hiring Bioinformatics Software Engineer in United States

PacBio’s Application Software Group focuses on building solid, strategic value around our core data type – highly accurate, long read sequencing – by producing innovative software that unlocks genomics in ways never seen before. We’re growing an interdisciplinary team of bioinformatic experts to tackle some of the most interesting problems…

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Assistant Research Professor – Genomics and Bioinformatics job with City of Hope

About City of Hope City of Hope, an innovative biomedical research, treatment and educational institution with over 6000 employees, is dedicated to the prevention and cure of cancer and other life-threatening diseases and guided by a compassionate, patient-centered philosophy. Founded in 1913 and headquartered in Duarte, California, City of Hope…

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Mapping digested synthetic oligos back to original sequences.

Mapping digested synthetic oligos back to original sequences. 0 Hi, I have several synthetic dsDNA of 70bp and I digest them with some enzyme. I am interested to see the exact cut site of the enzyme so I had the products sequenced using MiSeq. They are single-end read. What is…

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How can I extract base and read name based on position from bam file?

How can I extract base and read name based on position from bam file? 0 Hello. Sadly, I can’t not use English well…. I want to make primer for many cultivar of my subject. In my primer position, there are two bialleic SNP. ex) …..A/C……….C/G…….. I think reason of this…

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How to align and visualize data with .fasta and .gff3 files in IGV?

How to align and visualize data with .fasta and .gff3 files in IGV? 1 Hi everyone, I have an issue in aligning and visualizing my data in IGV. As I read in manual of IGV, to align and visualize data, I need to to prepare .BAM/.SAM or other input format…

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Metadata for splice variant VCF

Metadata for splice variant VCF 0 Hi all, I am making manual VCF for splice site Variant using IGV tool.. I can make the VCF fine but I don’t know that meta data required for splice variants VCF . Small variant vcf metadata is not working as I am not…

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Vcfutils error code

Vcfutils error code 20-08-2021 code at line (I think) just to get it to write a proper fq. Second issue is this error: substr outside of string at /usr/local/bin/object91.ru line We can do this in a single…

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How to use IGV (or any genome vis tool) show normalised ChIP-Seq peak intensity?

How to use IGV (or any genome vis tool) show normalised ChIP-Seq peak intensity? 1 Hi everyone: I have a question about IGV, I am quite new on ChIP-seq data. Question: In analysis side, I use MACS2 for peak calling, MAnorm2 for normalisation. etc, the result looks good. In IGV…

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from genome position to protein position

from genome position to protein position 0 Hello, Does anyone know a tool to go from genomic positions to protein and to see whether SNPs are (non)synonymous in bacteria? Doing it manually in IGV would take too much time… I have experience with Python, R and bash. Thanks in advance,…

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Biostar Systems

Comment: STAR vs Novoalign IGV Browser visualization by chasem &utrif; 10 That is good to know that it isn’t just my set of reads…still concerning, though. Comment: STAR vs Novoalign IGV Browser visualization by chasem &utrif; 10 I was not expecting this — not sure what to make of it…

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STAR vs Novoalign IGV Browser visualization

STAR vs Novoalign IGV Browser visualization 0 I feel a bit silly about this, but I’m having trouble finding information on the horizontal lines which appear with STAR alignments, but not novoalign alignments. Could anyone help point me in the right direction for documentation on what these mean? These are…

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Mapping quality and XS score

Mapping quality and XS score 0 Hi, I am currently looking through bam files using igv to manually check if the mutations not called by Mutect2 are really an error or not. Until now, to filter reads with low quality, I have used only MAPQ > 30 and didn’t consider…

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How to change the track background color of IGV

How to change the track background color of IGV 0 Somehow IGV’s default background is not white. When I take a screenshot from IGV and put it onto powerpoint, I can clearly see that IGV is kinda grey-ish. I was wondering if there is a simple toggle to make IGV…

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Error when trying to run IGV on server

Error when trying to run IGV on server 1 I want to use IGV on a server so I don’t have to download bam files to my local machine. I used conda to install igvtools. When I type igvtools in the command line I get this error: Using system JDK….

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Ten simple rules for biologists initiating a collaboration with computer scientists

I think it depends. I think it is probably quite a good guide for Bioinformaticians that want to collaborate with “proper” computer scientists when they need new computer science to solve their problems. I think its less good for biologists who need to collaborate with someone to give more computational…

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I am converting the fq.gz. files (which are the results of the mgi study) to bam files to view on igv.

I am converting the fq.gz. files (which are the results of the mgi study) to bam files to view on igv. 0 Hey everyone, before i start apologies for the inconvenience cause of my wrong or inappropriate use of terms. I take some fails of bwa mem lately. As i…

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