Tag: UCSC

Reference genome, BWA and right algorithm

Reference genome, BWA and right algorithm 1 Hello I’m using BWA to create the index for aligning some rna-seq fastq. First thing I did was download hg38.fa.align.gz from UCSC Then I: gzip -d hg38.fa.align.gz sudo apt-get install bwa Here comes the problem. BWA instructions reccomend bwtsw algorithm, but when I…

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ChIP-seq peak track loading error on hg38 genome

Dear UCSC genome browser team, Thank you for public sharing comprehensive and very useful data sets in UCSC genome browser. I’d like to report the error in UCSC genome browser. When I have access to ChIP-seq tracks on UCSC genome browser to visualize TF peaks (e.g., KLF5, ATF3), currently the UCSC…

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ENCODE ChIP-seq peak track loading error on hg38 genome

Dear UCSC genome browser maintainers,   Hi. Thank you for public sharing comprehensive and very useful data sets in UCSC genome browser.   I’d like to report the error in UCSC genome browser. When I have access to ENCODE ChIP-seq tracks on UCSC genome browser to visualize TF peaks (e.g.,…

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Bioconductor T2T-CHM13

Comment: Reduce single cell experiment size to use as reference for annotation with Singl by elgomez • 0 Thank you, James! I ended up running seurat FindVariableFeatures with nfeatures = 10000 and then subsetting the object to just those varia… Comment: Help with model.matrix and creating the right contrast matrix…

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Convert bed file from hg19 to GRCH38

Convert bed file from hg19 to GRCH38 1 Hello everyone! I have a list of over 500,000 rs and I would like to obtain the coordinates (BED file) on the GRCH38 reference genome. I am using the UCSC Table Browser tool, but unfortunately, it doesn’t find 90,000 rs, and since…

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overlapping duplicate dispersed_repeat feature in stringtie

GFF Error: overlapping duplicate dispersed_repeat feature in stringtie 0 Hi. I got following error when I use stringtie. with repeatmasker annotation gff file and RNA-seq bam files which is already sorted with samtools. GFF Error: overlapping duplicate dispersed_repeat feature (ID=461) GFF Error: overlapping duplicate dispersed_repeat feature (ID=712) GFF Error: overlapping…

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AstraZeneca Bioinformatics Job – Bioinformatics Consultant Post

“Unlock Your Potential: Join AstraZeneca as a Bioinformatics Consultant and Revolutionize Drug Discovery!” –Must See– AstraZeneca Bioinformatics Job Job Post: Consultant – Bio Informatician At AstraZeneca, our mission is to improve the quality of healthcare and make a positive impact on the lives of millions of patients. We are seeking…

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Merge two bigwig(+/- strand) files from RNA-seq

Merge two bigwig(+/- strand) files from RNA-seq 2 Hi all, I am working on expression data from EpigeneticRoadmap and wanted to generate an expression track.(Link here) Since the cell line expression data only has bigwig file in two separate files. One from positive strand; the other from negative strand and…

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Bioconductor – BSgenome.Tguttata.UCSC.taeGut1

DOI: 10.18129/B9.bioc.BSgenome.Tguttata.UCSC.taeGut1     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Tguttata.UCSC.taeGut1. Full genome sequences for Taeniopygia guttata (UCSC version taeGut1) Bioconductor version: 3.14 Full genome sequences for Taeniopygia guttata (Zebra finch) as provided by UCSC (taeGut1, Jul. 2008) and stored in…

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Multi-factor designs in DiffBind

Multi-factor designs in DiffBind 1 Dears, I’m trying to analyze some ChIPseq data using DiffBind. Samples has been processed in two different times SampleID Name Factor IP Condition Replicates 5 PBS_Pol2 S3 Batch1 Pol2 PBS 1 6 PBS_Pol2 S9 Batch2 Pol2 PBS 2 7 C26_Pol2 S4 Batch1 Pol2 C26 1…

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ClinVar and DGV

Hello, we are using UCSC in micro array reading support to help us evaluate CNVs but, this morning, the DGV and ClinVar databases have disappeared. The cause of this is an update and then everything will go back to the way it was before or will it stay that way…

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Human hg38 chr6:31,165,200-31,165,800 UCSC Genome Browser v457

     Custom Tracks ac4C-RIP-seq peaks, hESC CTL-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC CTL-2hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-2hidedensesquishpackfull    Mapping and Sequencing Base Positionhidedensefull p14 Fix Patcheshidedensesquishpackfull p14 Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19…

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Bioconductor – BSgenome.Rnorvegicus.UCSC.rn7 (development version)

DOI: 10.18129/B9.bioc.BSgenome.Rnorvegicus.UCSC.rn7   This is the development version of BSgenome.Rnorvegicus.UCSC.rn7; for the stable release version, see BSgenome.Rnorvegicus.UCSC.rn7. Full genome sequences for Rattus norvegicus (UCSC genome rn7) Bioconductor version: Development (3.19) Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (genome rn7) and stored in Biostrings objects. Author: The…

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Chapter 6 GGHH 2023 – notes – Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes

Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes Define an eQTL Summarise the methodology of RNAseq Understand the reason for expressing RNAseq outcomes as transcripts per million (TPM) Explain why patterns of H3K4me3 and H3K27ac can be used as markers of transcriptionally active genes Incorporate this data into a…

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Fastest way to convert BED to GTF/GFF with gene_ids?

This is probably a duplicated question from: How To Convert Bed Format To Gtf? How to convert original BED file to a GTF ? Converting different annotation file formats (GTF/GFF/BED) to each other How to change scaffold.fasta file or scaffold.bed file to GTF file? Convert bed12 to GFF convert bed12…

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Senior Bioinformatics Systems Analyst in Santa Cruz, CA for University of California Santa Cruz

Details Posted: 01-Dec-23 Location: Santa Cruz, California Salary: Open Categories: Information Technology Staff/Administrative Senior Bioinformatics Systems Analyst Location: Santa CruzJob ID: 61781 JOB POSTING NO VISA SPONSORSHIP IS AVAILABLE FOR THIS POSITION.THIS RECRUITMENT WILL REMAIN OPEN UNTIL FILLED. HOW TO APPLY For full consideration, applicants should attach their resume and…

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Scientists unearth secrets of the world’s smallest porcupine species

Scientists conducted the first investigation in 22 years into the Roosmalen’s dwarf porcupine, an elusive forest porcupine in Brazil. With the fresh tissue of a new specimen, the scientists used the porcupine’s DNA sequence and physical traits to better trace its relationship to other species. Their discovery shows the porcupines…

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WO2017055487A2 – A METHOD FOR DIAGNOSING A DISEASE BY DETECTION OF circRNA IN BODILY FLUIDS

“Current Protocols in Molecular Biology“, 1991, JOHN WILEY & SONS, pages: 6.3.1 – 6.3.6 “Quantitative monitoring of gene expression patterns with a complementary DNA microarray.“, SCIENCE, vol. 270, no. 5235, 1995, pages 467 – 70 ALTSCHUL ET AL., J. MOL. BIOL., vol. 215, 1990, pages 403 – 410 ALTSCHUL ET…

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Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-voom

Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-voom 0 Hi everyone, first of all, I’m new for bioinformatics. I have downloaded RNAseq data of TCGA-LUAD from UCSC that had already normalized RSEM normalized count and log2 transformed (log2 normcount+1). i wonder if i can…

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Where do these snpeff annotation come from?

Where do these snpeff annotation come from? 0 I am annotating a VCF with annotation from snpeff, which I want to use eventually to parse for predicted loss of function variants I want to understand the annotation better and document how they are happening. I run this command: snpEff “hg38″…

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Tricorder Tech: UCSC Astrobiologist David Deamer And Mark Akeson Honored For Invention Of Nanopore Sequencing

UCSC’s David Deamer and Mark Akeson won the Golden Goose award for the invention of nanopore sequencing, a transformational technology for reading DNA and RNA. Here, Deamer holds the MinION, a portable device for nanopore sequencing. (photo by Nick Gonzales) [In September 2023] two UC Santa Cruz researchers were honored…

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hg38 RepeatMasker v4.0.7 Dfam_2.0 question

Dear UCSC Genome Browser Support Team:   I hope this message finds you well.   I am writing to you as a postdoctoral researcher from Dr. Xianjun Dong’s Lab at Harvard Medical School. Firstly, I would like to extend my heartfelt gratitude for your significant efforts in developing the human…

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Bioconductor – ind1KG

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see ind1KG. Data from 1000 Genomes, NA19240 (female) chr6 excerpt Bioconductor version: 2.13 Elements of samtools/bioc workflow for dealing with personal sequence focusing on identification and interpretation of rare variants Author: VJ Carey <stvjc…

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Chipseq peak calling and peak frequency region

I am working on Chip seq data, I have implemented the chipseq pipeline with spike in method and called peaks using MACS2. The same data has been analyzed before in my lab, and my peaks show a similar pattern as the previous ones . By this I meant that the…

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Bioconductor – gDNAx

DOI: 10.18129/B9.bioc.gDNAx   Diagnostics for assessing genomic DNA contamination in RNA-seq data Bioconductor version: Release (3.18) Provides diagnostics for assessing genomic DNA contamination in RNA-seq data, as well as plots representing these diagnostics. Moreover, the package can be used to get an insight into the strand library protocol used and,…

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CRISPR-Cas9 Gene Editing Is On The Cusp Of Something Big

Natali_Mis Gene editing, also known as genome editing, is a method where the DNA of an organism is modified using biotechnological techniques. It allows scientists to add, remove, or alter genetic material at particular locations in the genome. This 2-part series will cover the basics of CRISPR-Cas9 (see below) in…

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Analyzing somatic mutations by single-cell whole-genome sequencing

Failla, G. The aging process and cancerogenesis. Ann. N. Y. Acad. Sci. 71, 1124–1140 (1958). Article  CAS  PubMed  Google Scholar  Szilard, L. On the nature of the aging process. Proc. Natl Acad. Sci. USA 45, 30–45 (1959). Article  CAS  PubMed  PubMed Central  Google Scholar  Vijg, J. & Dong, X. Pathogenic…

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Is there a way to query Ensembl to get all 3’UTRs from all species?

Is there a way to query Ensembl to get all 3’UTRs from all species? 1 I am trying to obtain stats on how many 3’UTRs are annotated in Ensembl. I would really like to download the as many annotated 3’UTRs as possible from as many species as possible and find…

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How to obtain data on the coordinates of the Exon region from UCSC

How to obtain data on the coordinates of the Exon region from UCSC 1 UCSC is accessible via MySQL (genome.ucsc.edu/goldenPath/help/mysql.html) and I’ve always found it very useful to browse tables this way to see exactly what is contained in a specific table within a specific database. I use Sequel Pro…

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Data for non-human primates

Data for non-human primates 0 Hi everyone, I have two questions regarding data/annotations (parallel to human) for non-human primates: The GENCODE gene annotation file provides very comprehensive gene annotation but GENCODE has files only for human and mouse. Can I find some parallel file for non-human primates from any resource?…

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UCSC Genome Browser Custom Track Blank

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…

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GISTIC isn’t checking chromosome 23 / X

GISTIC isn’t checking chromosome 23 / X 0 Hi, I have a problem with GISTIC apparently not checking for CNV on chromosome X. GISTIC2 runs without errors on my segmentation file with the supplied reference file refgenefile=refgenefiles/hg38.UCSC.add_miR.160920.refgene.mat My input file has CNV events in chromosome ’23’ but the GISTIC run…

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How to change "CompressedGRangesList" to "GRangesList"

Hi, I am trying to A/B compartment analysis with minfi, but I got following error. “`r Error in { : task 1 failed – “is(object, “SummarizedExperiment”) is not TRUE” “` Since I want to use data with hg38 annotation but `makeGenomicRatioSetFromMatrix` function has only `ilmn12.hg19`, I did `makeGenomicRatioSetFromMatrix` function with…

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Senior Bioinformatician – Centogene, Berlin or Remote

Senior Bioinformatician – Centogene, Berlin or Remote Senior Bioinformatician Centogene Berlin or Remote, Germany Your tasks and responsibilities: We are looking for senior Bioinformatician to join in the R&D bioinformatics team in either Berlin or remotely from all over the world. You will be responsible for developing new bioinformatics pipelines…

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Bioconductor – CAGEr

DOI: 10.18129/B9.bioc.CAGEr     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see CAGEr. Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining Bioconductor version: 3.9 Preprocessing of CAGE sequencing data, identification and…

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Bioconductor – TxDb.Hsapiens.UCSC.hg38.knownGene

DOI: 10.18129/B9.bioc.TxDb.Hsapiens.UCSC.hg38.knownGene     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see TxDb.Hsapiens.UCSC.hg38.knownGene. Annotation package for TxDb object(s) Bioconductor version: 3.9 Exposes an annotation databases generated from UCSC by exposing these as TxDb objects Author: Bioconductor Core Team, Bioconductor Package Maintainer <maintainer at…

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Bioconductor – BSgenome.Hsapiens.UCSC.hg19.masked

    This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Hsapiens.UCSC.hg19.masked. Full masked genome sequences for Homo sapiens (UCSC version hg19) Bioconductor version: 3.3 Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects….

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Bioconductor – BSgenome.Cfamiliaris.UCSC.canFam2

DOI: 10.18129/B9.bioc.BSgenome.Cfamiliaris.UCSC.canFam2   Full genome sequences for Canis lupus familiaris (UCSC version canFam2) Bioconductor version: Release (3.18) Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam2, May 2005) and stored in Biostrings objects. Author: The Bioconductor Dev Team Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation…

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Bioconductor – AnnotationHub

DOI: 10.18129/B9.bioc.AnnotationHub     Client to access AnnotationHub resources Bioconductor version: Release (3.6) This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be…

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Zebrafish danRer11 chr6:43,426,661-43,433,266 UCSC Genome Browser v456

     DANIO-CODE Track Hub 3P-seq trackshidedensesquishpackfull CAGE-seq trackshidedensesquishpackfull ChIP-seq trackshidedensesquishpackfull RNA-seq trackshidedensefull Cell Typeshidedensesquishpackfull Consensus promotershidedensesquishpackfull Conservation and CRISPR targetshideshow COPEs and pooled DOPEshideshow Enhancer validationhideshow HiC trackshidedensefull Stages_Typeshidedensesquishpackfull    Mapping and Sequencing Base Positionhidedensefull Assemblyhidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Incidenthidedensesquishpackfull INSDChidedensesquishpackfull RefSeq Acchidedensesquishpackfull Restr Enzymeshidedensesquishpackfull Short Matchhidedensesquishpackfull   …

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Question about directly posting small custom tracks to UCSC genome browser

Hello UCSC Genome Browser Team, I’m writing to query about a change in API function I’ve noticed sometime over the course of this year. I want to see if the functionality has been intentionally removed, or may be either a bug on my side or your side. …

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UCSC custom track upload direct data POST / without url

Hello All, Documentation seems rather scarce on this topic so I just come here to find a consensus. In some software I write for the lab I’m in, there is a feature to view on UCSC. This feature will create a small BED file (usually ~10-20 lines), upload to UCSC…

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About the item name of UCSC GWAS catalog

hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gwasCatalog.sql `bin` smallint(5) unsigned NOT NULL, `chrom` varchar(255) NOT NULL, `chromStart` int(10) unsigned NOT NULL, `chromEnd` int(10) unsigned NOT NULL, `name` varchar(255) NOT NULL, `pubMedID` int(10) unsigned NOT NULL, `author` varchar(255) NOT NULL, `pubDate` varchar(255) NOT NULL, `journal` varchar(255) NOT NULL, `title` varchar(1024) NOT NULL, `trait` varchar(255) NOT NULL, `initSample`…

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Genome Browser Chimera Interface

Download Chimera Configure for automatic launch in web browsers UCSF Chimera is an interactive molecular modeling system that supports 3-D visualization of protein structures.It runs as an application on the user’s computer. The UCSC Genome Browser provides links to launch Chimera as a helper application for proteins with solved structures…

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zero counts for all genes in RNAseq data of Ferret

zero counts for all genes in RNAseq data of Ferret 0 I have bulk RNAseq data from Ferret and trying to get counts per gene. to do so I used hisat2 and got the genome from here: hgdownload.soe.ucsc.edu/goldenPath/musFur1/bigZips/musFur1.2bit after aligning the fastq files I used htseq and the following command:…

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DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle

Overview of this study In this study, we measured the DNA methylome from mouse liver and skeletal muscle, integrated the data with the transcriptome and proteome of these mouse tissues22,23, and examined how tissue-dominant protein and gene expression were associated with DNA hypomethylation (Fig. 1). In this study, we measured DNA…

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[genome-www] Where can we find Repeats Fasta for CAST_EiJ genome assembly?

Hi Matthew and Robert,   HNY!  I have a question for the UCSC Genome Browser Help Desk I was wondering if you could advise us how to do this.  I downloaded the table information for the Track NumtS Sequence from the Group Variations and Repeats from the Mouse mm9 Assembly…

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Is the UCSC bus free?

Is the UCSC Bus Free? Yes, the UCSC bus is free for students, staff, and faculty members. Whether you are commuting to campus or planning to explore the Santa Cruz area, the UCSC bus system offers convenient and cost-effective transportation options. The UCSC bus system, also known as the Metro…

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Add r-bsgenome-hsapiens-ucsc-hg38-masked and r-dnamcrosshyb.

* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg38-masked): New variable. Change-Id: Ic1b646a3bd3b7262dd82f0972961c2e89628e90b — gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) Toggle diff (51 lines) diff –git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d79236ea26..ac09a079b4 100644 — a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -68,6 +68,42 @@ (define-module (gnu packages bioconductor) ;;; Annotations +(define-public r-bsgenome-hsapiens-ucsc-hg38-masked + (package + (name “r-bsgenome-hsapiens-ucsc-hg38-masked”) +…

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Characterization of H3K9me3 and DNA methylation co-marked CpG-rich regions during mouse development | BMC Genomics

CHMs are stable during mouse development To explore the co-localization between H3K9me3 and DNA methylation, we collected public H3K9me3 chromatin immunoprecipitation sequencing (ChIP-seq) and whole-genome bisulfite sequencing (WGBS) data during mouse pre-implantation embryogenesis [11], PGC development [12], spermatogenesis [13, 14], retina development [15], heart and liver development after gastrulation [16,17,18]…

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Extracting the near amino acid number from an essential splice site variant

Extracting the near amino acid number from an essential splice site variant 1 Hi all, I have some essential splice site variants, and I am trying to find a systematic way to derive the nearest amino acid number to the variants. For example, I have 1:6522052:A:G (GRCh37), and it’s HGVS…

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Bioconductor – EpiTxDb

DOI: 10.18129/B9.bioc.EpiTxDb   Storing and accessing epitranscriptomic information using the AnnotationDbi interface Bioconductor version: Release (3.18) EpiTxDb facilitates the storage of epitranscriptomic information. More specifically, it can keep track of modification identity, position, the enzyme for introducing it on the RNA, a specifier which determines the position on the RNA…

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How measure the specificity of RT-qPCR primers

RT-qPCR primer specificity can be measured using a bioinformatics workflow that involves analyzing potential mismatches, cross-matches, co-amplification of multiple gene splice variants, and sub-optimal amplicon sizes in silico. This workflow utilizes publicly available resources such as NCBI Primer BLAST, in silico PCR in UCSC genome browser, and Ensembl DNA database…

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Unable to Generate Motif class for zebrafish scATAC data using Signac package.

Unable to Generate Motif class for zebrafish scATAC data using Signac package. 0 Hi, I am analyzing zebrafish scATAC data using Signac package. The package does not allow me to create motif class. It gives me the following error after running AddMotif function. `ATAC <- AddMotifs( object = ATAC, genome…

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Genome Assembly no matches

Genome Assembly no matches 1 I am very new to this and am matching primers to the genome assembly and GENCODE before running PCR. When targeting the “GENCODE Genes” I get a successful output of 170 bp. However, when targeting “genome assembly”, I get no matches. What does this mean,…

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CIMB | Free Full-Text | mtDNA Single-Nucleotide Variants Associated with Type 2 Diabetes

1. Introduction Type 2 diabetes (T2D) is the most prevalent metabolic disease and a significant public health concern [1,2], leading to early-onset disability and elevated mortality due to various related complications [3]. Between 1990 and 2017, the global trend in the age-standardized rates of T2D, as measured by the number…

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Bioconductor – plyinteractions

DOI: 10.18129/B9.bioc.plyinteractions   Extending tidy verbs to genomic interactions Bioconductor version: Release (3.18) Operate on `GInteractions` objects as tabular data using `dplyr`-like verbs. The functions and methods in `plyinteractions` provide a grammatical approach to manipulate `GInteractions`, to facilitate their integration in genomic analysis workflows. Author: Jacques Serizay [aut, cre] Maintainer:…

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Bioconductor – regioneR (development version)

DOI: 10.18129/B9.bioc.regioneR   This is the development version of regioneR; for the stable release version, see regioneR. Association analysis of genomic regions based on permutation tests Bioconductor version: Development (3.19) regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other…

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Mouse mm10 chr4:22,481,383-22,489,763 UCSC Genome Browser v455

     Custom Tracks Adiposehidedensesquishpackfull Cerebellumhidedensesquishpackfull Cortexhidedensesquishpackfull Liverhidedensesquishpackfull Lunghidedensesquishpackfull Sintesthidedensesquishpackfull Spleenhidedensesquishpackfull    mouse_7_core ATAC Adipose Rep1hidedensefull ATAC Adipose Rep2hidedensefull ATAC Cerebellum Rep1hidedensefull ATAC Cerebellum Rep2hidedensefull ATAC Colon Rep1hidedensefull ATAC Colon Rep2hidedensefull ATAC Cortex Rep1hidedensefull ATAC Cortex Rep2hidedensefull ATAC Heart Rep1hidedensefull ATAC Heart Rep2hidedensefull ATAC Liver Rep1hidedensefull ATAC Liver Rep2hidedensefull ATAC…

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Bioconductor – regionalpcs (development version)

DOI: 10.18129/B9.bioc.regionalpcs   This is the development version of regionalpcs; for the stable release version, see regionalpcs. Summarizing Regional Methylation with Regional Principal Components Analysis Bioconductor version: Development (3.19) Functions to summarize DNA methylation data using regional principal components. Regional principal components are computed using principal components analysis within genomic…

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Genomic signatures of convergent shifts to plunge-diving behavior in birds

Wyles, J. S., Kunkel, J. G. & Wilson, A. C. Birds, behavior, and anatomical evolution. Proc. Natl Acad. Sci. 80, 4394–4397 (1983). Article  CAS  PubMed  PubMed Central  Google Scholar  Lapiedra, O., Sol, D., Carranza, S. & Beaulieu, J. M. Behavioural changes and the adaptive diversification of pigeons and doves. Proc….

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Error regarding fetching “hguid” cookie

Hello,  I am wondering if fetching data from UCSC is currently unavailable, because when I use the R/Bioconductor packages Gviz and rtracklayer, I receive the following same error.  1. library(Gviz) IdeogramTrack(genome=”hg38″,chromosome=”chr16″,fontsize=30,Gviz.ucscUrl=”genome.ucsc.edu/cgi-bin“)# Error in .local(.Object, …) : Failed to obtain ‘hguid’ cookie 2. library(Gviz) cpgIslands <- UcscTrack(genome = “hg38”, chromosome =…

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rtracklayer error for browserSession UCSC

rtracklayer error for browserSession UCSC 1 @f64e2e65 Last seen 16 hours ago Germany An older error from rtracklayer has resurfaced. When calling a browserSession, it gives the error below. I assume this is due to a URL problem, possibly when trying to connect to UCSC from Europe. Could someone please…

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How do I write a correctly formatted gff3 file in R?

Dear all, I am trying to annotate non-coding RNA in a small RNA-seq dataset. The RNACentral gff3 file that I am using has different chromosome identifiers than the genome assembly. I have loaded the gff3 file in R where I changed the chromosome identifiers using the the assembly report and…

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Using injectSNPs with a custom set of SNPs

Using injectSNPs with a custom set of SNPs 1 @steve-pederson-23427 Last seen 14 hours ago Australia Hi, I’m sorry if this is a dumb question, but I have a set of SNPs obtained from a large cohort study which can’t be released as a SNPlocs package. Is there any way…

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Systematic differences in discovery of genetic effects on gene expression and complex traits

Claussnitzer, M. et al. A brief history of human disease genetics. Nature 577, 179–189 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190–1195 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Gusev, A. et…

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how to get genomic locations of Sequence patterns in R

Hi, my current implementation returns the indexes of input genomic range where “CG” are found but i want to get the genomic location matching the pattern. pls see code and example data. thank you in advance for your help getMotif_sites <- function(ref_genome=NULL, grList=NULL, context=”CG”){ library(Biostrings) # Load ref genome of…

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Genome Browser Git Access

Install Git:Install Git software version 1.6.2.2 or later. See the Git Community Handbook installation and setup instructions, as well as our Installing git Genomewiki page. Start an initial Git local repository: $ git clone Or, if a firewall prevents git daemon port 9418, use: $ git clone genome-source.soe.ucsc.edu/kent.git The…

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E-IT hiring Bioinformatics Business Analyst in United States

Company Description E-IT Professionals Corp. (EIT) is an award-winning IT consulting, recruitment, management, and staffing organization founded in 1999. EIT is comprised of around 320 Information Technology Consultants and boasts revenues approaching $21M overall. Our dedicated team of professionals in the US and India serves clients from various geographies. We…

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Part time Bioinformatics Job?

Job:Part time Bioinformatics Job? 0 Hi, My name is Imon and I am looking for a part time bioinformatics position. Remote only. About 20 hours per week is what I’m looking for. Ideally I SSH into your server to do research and ideally you have multiple cores and threads. I…

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Bioconductor – easylift (development version)

DOI: 10.18129/B9.bioc.easylift   This is the development version of easylift; to use it, please install the devel version of Bioconductor. An R package to perform genomic liftover Bioconductor version: Development (3.18) The easylift package provides a convenient tool for genomic liftover operations between different genome assemblies. It seamlessly works with…

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How to obtain data on the specific location of the segumental duplication.

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…

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How To Find The Enriched Repeat Elements Between Two Sequences

How To Find The Enriched Repeat Elements Between Two Sequences 2 Hi, I want to know which repeat element is statistically enriched in one sequence compared to the background sequence, how should I perform such a statistic calculate? For repeat data, I have got bed format repeatmasker from UCSC.For example,…

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Bioconductor – GreyListChIP

DOI: 10.18129/B9.bioc.GreyListChIP     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see GreyListChIP. Grey Lists — Mask Artefact Regions Based on ChIP Inputs Bioconductor version: 3.11 Identify regions of ChIP experiments with high signal in the input, that lead to spurious peaks during…

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UCSC Genome Browser hg38 and COSMIC v98 records

Hello, I have a question; why are the v98 COSMIC records for these two variants: NM_005228.5(EGFR):c.2062-3del NM_005228.5(EGFR):c.2062-3dup displayed in different coordinates in the UCSC genome browser hg38? (The Position: and Genomic coordinates also differ here: Genome Browser …919-…919 and COSMIC …918-…919 Additionally, for…

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How to get RPKM from count matrix

How to get RPKM from count matrix 0 Hi Biostars, I have a count matrix with mouse gene name and need to get RPKM. I know it is not a good metric but biologists used to it. gtf <- readGFF(“/reference_genome/mm39.ncbiRefSeq.gtf”) gtf_exon <- gtf[gtf$type == “exon”, ] width <- gtf_exon$end -…

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Experiment genomics- expasy, plasmapper, primer blast, ucsc – EXPERIMENT- AIM- analysis of UCSC

EXPERIMENT-1 AIM– analysis of UCSC BROWSER and retrieving a gene from a desired chromosome position. Database- UCSC GENOME BROWSER Steps 1. Open the UCSC Brower. 2. Click on genome browser. 3. Choose genome-asia.ucsc.edu 4. Choose human from species. 5. Choose the latest genome assembly – Dec. 2013 (GRCh38/hg38) 6. Enter…

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UCSC iGEM 2023 addressing harmful algal blooms through synthetic biology

This year’s team of student innovators, members of the UCSC International Genetically Engineering Machine (iGEM) program, is addressing a local yet widespread environmental issue: harmful algal blooms in Watsonville’s Pinto Lake. The team’s bioengineering approach targets the toxic genes of the specific bacteria responsible for the algal blooms, creating a…

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How Do I Convert From Bed Format To Gff Format?

How Do I Convert From Bed Format To Gff Format? 4 I have a file in GFF format and I need to convert it to BED format. What do I do? bed gff galaxy • 29k views Both formats are tab delimited text files used to represent DNA features in…

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OmniAb, Inc. hiring Senior Bioinformatics Scientist in Emeryville, California, United States

We are seeking a Senior Bioinformatics Scientist to support our ongoing antibody discovery and genetic engineering efforts. The role includes refining custom tools and algorithms to facilitate identification of therapeutic leads from OmniAb immune repertoires and applying cutting edge computational biology approaches to all stages of antibody discovery, from antigen…

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Epidemiology and analysis of SARS-CoV-2 Omicron subvariants BA.1 and 2 in Taiwan

Prevalence of Omicron subvariants between December 2021 and January 2023 in Taiwan BA.1 and BA.2 and their sublineages entered Taiwan in December 2021 and January 2022, respectively (Supplementary Table S1 and Fig. 1). These two Omicron lineages did not cause COVID-19 outbreaks until March and April 2022 (Supplementary Table S1 and…

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Bioconductor – SNPlocs.Hsapiens.dbSNP142.GRCh37

DOI: 10.18129/B9.bioc.SNPlocs.Hsapiens.dbSNP142.GRCh37     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see SNPlocs.Hsapiens.dbSNP142.GRCh37. SNP locations for Homo sapiens (dbSNP Build 142) Bioconductor version: 3.13 SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 142. The source data files used for…

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Genome B HW.docx – MCB 3400 Spring 2023 Lab 1: Simple genomic data analysis The main purpose of this exercise is for you to become more familiar with

MCB 3400 Spring 2023 Lab 1: Simple genomic data analysis The main purpose of this exercise is for you to become more familiar with visualizing and analyzing simple genomic data and exploring gene models. 1. Explore the UCSC genome browser Go to UCSC genome browser webpage at . Click “Genomes”…

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PTEN-induced kinase 1 gene single-nucleotide variants as biomarkers in adjuvant chemotherapy for colorectal cancer: a retrospective study | BMC Gastroenterology

Tissue samples A total of 84 analytic samples from surgical or biopsy specimens were collected from 84 patients who underwent radical surgery for CRC at Saitama Medical University International Medical Center between January and December 2016. One case was excluded because the specimen was too small; therefore, we used a…

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UCSC’s David Deamer and Mark Akeson honored for invention of nanopore sequencing

David Deamer (left) and Mark Akeson in Santa Cruz in 2023 after receiving the inaugural UCSC Chancellor’s Innovation Impact Award for inventing nanopore sequencing. (photo by Nestor Guerrero) September 27, 2023 By Emily Cerf UCSC’s David Deamer and Mark Akeson won the Golden Goose award for the invention of nanopore sequencing, a…

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i don’t know error UCSC hg38.fa reference

i commend in  sequenza-utils bam2seqz -p –normal ${RESULTS}/5_variant_calling/${sample}_N.mpileup –tumor ${RESULTS}/5_variant_calling/${sample}_T.mpileup –fasta ${REFER}/hg38.fa -gc ${REFER}/hg38_genome_gc50.wig.gz -o ${RESULTS}/8_seq/${sample}_seqz.gz sequenza-utils seqz_binning  –seqz ${RESULTS}/8_seq/${sample}_seqz.gz -w 50 -o ${RESULTS}/8_seq/${sample}_small_seqz.gz results in dictory chromosome_depth.pdf, gd_plot.pdf, sequenza_extract.RData  chromosome_depth.pdf chromosome chr 1,10,11, chr11_ KI270721v1_random… Why is it in the result file chr 2 ~xy  ? Read more…

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Troubles launch IGV on Linux(Debian)

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…

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NVIGEN Pioneers Breakthrough in High-Resolution Tissue RNA Sequencing with Magnetic Nanoparticle Capture from Nanopipetting Aspiration of Minuscule Single Cell Contents

SANTA CLARA, Calif., Sept. 26, 2023 /PRNewswire/ — NVIGEN, a leading provider of modern nanoparticle solutions to empower revolutionary personalized healthcare, announces its new application in RNA sequencing (RNAseq) that promises to transform our understanding of cellular dynamics within tissues. Single-cell transcriptomics have opened new frontiers in…

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Calculation of TMB on gene level

Calculation of TMB on gene level 1 Hi all, I have TCGA cancer data and i want to calculate TMB on gene level. Can anyone please tell me how to do that? TCGA has TMB score based on patient level. I need on gene level. Thanks! genomics • 30 views…

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Fibroblast Growth Factor Receptor 2 (FGFR2), a New Gene Involved in the Genesis of Autism Spectrum Disorder

The ASD patient described here showed a mutation in the FGFR2 gene, located in the chromosomal band 10q26 (Fig. 1a) and encoding the fibroblast growth factor receptor type 2. It belongs to the family of tyrosine kinase receptors (including FGFR1, FGFR3, and FGFR4) that regulate several biological processes, including bone development,…

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Research Engineer Position in Bioinformatics at Institut Pasteur Paris – Institut Pasteur de Paris – Neuroscience – portail emploi

Research Engineer Position in Bioinformatics at Institut Pasteur Paris – Research – Institut Pasteur” Postdoctoral Researcher in Computational Biology / Bioinformatician Engineer Post-Doctoral Researcher Position in phylogenomics and pangenomics Emploi Research Engineer Position in Bioinformatics at Institut Pasteur Paris Équipe: Hub de Bioinformatique et Biostatistique Équipe: Interactions cerveau-immunité Département de:…

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Permanent Engineer Position in Bioinformatics at Institut Pasteur in Paris

The Bioinformatics and Biostatistics Hub at Institut Pasteur is hiring a permanent (CDI) research engineer in bioinformatics, who will be attached to the Mechanisms of Epigenetic Inheritance Laboratory headed by Dr. Germano Cecere.  The engineer will dedicate 80% of their time to work in the team headed by Dr. Germano Cecere.  The remaining 20% will be devoted to technical contribution, interaction with the Hub, and training…

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TxDb.Dmelanogaster.UCSC.dm3.ensGene

TxDb.Dmelanogaster.UCSC.dm3.ensGene 0 @3d4ffabd Last seen 1 day ago Egypt Enter the body of text here Code should be placed in three backticks as shown below getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘help(“repositories”, package = “BiocManager”)’ for details. Replacement repositories: CRAN: rspm/default/__linux__/focal/latest Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16) Installing…

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Using ExomeDepth for GRCH38 processed samples to call CNVs

The only difference would be the annotations, instead of using bedframes from data(genes.hg19) and data(exons.hg19) in ExomeDepth, I got them from the UCSC Table Browser for hg38 (genome.ucsc.edu/cgi-bin/hgTables). The only info they contain are: chromosome start end name ..and then run as before. Change bed.frame = exons.hg19 to the exon…

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Connection timing out when downloading hg19, mm10

Hi,   We are trying to setup a mirror of the UCSC browser.  The install went fine but when trying to download data we keep getting:  root@genome:/usr/install# bash browserSetup.sh mirror hg19 mm10 | | Downloading databases hg19 mm10 plus hgFixed/proteome/go from the UCSC download server | | Determining download file…

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Bioconductor – BSgenome.Rnorvegicus.UCSC.rn7

DOI: 10.18129/B9.bioc.BSgenome.Rnorvegicus.UCSC.rn7   Full genome sequences for Rattus norvegicus (UCSC genome rn7) Bioconductor version: Release (3.17) Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (genome rn7) and stored in Biostrings objects. Author: The Bioconductor Dev Team Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R,…

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Liftover GRCh37 to hg38 1kg/GATK.

Liftover GRCh37 to hg38 1kg/GATK. 1 I need to liftover a few variants from GRCh37 to hg38 1kg/GATK. UCSC lifover does not have this reference genome version available. I have tried with the standard hg38 but conversations are wrong. Where can I find GRCh37 to hg38 1kg/GATK chain files or…

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GTF annotation file for Hg38 Dec 2013 (First Release)

GTF annotation file for Hg38 Dec 2013 (First Release) 2 Hello, I am looking for the GTF file corresponding to the initial Dec. 2013 hg38 release. I have tried looking including here: hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/ but the directory does not contain the file (it does contain the original .fa file, though). I…

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Distance Tree For Gerp

Distance Tree For Gerp 3 I would like to calculate GERP scores for few genomic regions from non-model organism A (mammal). Lets assume I will get genomes from 10 other species, be it closely related to A, good quality genomic sequence, etc. Few questions: can I get some precalculated distance…

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How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols

Download a bed file for the canonical transcripts using UCSC Table Browser: track: UCSC Genes table: knownCanonical output format: select fields from primary and related tables press get output select fields from hg19.knownCanonical: chrom, chromStart, chromEnd, transcript select fields from hg19.kgXref: geneSymbol press get output The file UCSC_canonical.bed looks like:…

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