Categories
Tag: hg38
Moderate Mapping percentage
Moderate Mapping percentage 1 Hi all, I received my sequenced transcriptome and genomic data from my service provider and started working with it. Both the DNA and RNA data passed quality metrics post trimming. But the mapping percentage comes out to be 90% using bowtie-DNA and 85% using Hisat2-RNA. I…
The Evolution from HG19 to HG38
Welcome to another blog post! Reference genomes are essential benchmarks of a species’ genome that facilitate the accurate comparison of individual genomes and are crucial tools for identifying genetic variants and diagnosing rare diseases. Here, we will explore the evolution of the human reference genome, focusing on the transition…
Problem with DRAGEN RNAseq hashtable directory
Problem with DRAGEN RNAseq hashtable directory 1 Dear all, Recently I wrote a code to work with DRAGEN and RNAseq pipeline. I use this command: /opt/edico/bin/dragen -f -l \ -r refdir \ -1 ${forward} \ -2 ${reverse} \ -a ${gtf} \ –output-dir output/${sample} \ –output-file-prefix ${sample} \ –RGID ${sample}_group_id \…
BWA Index Referencing Failed. Possible Reason and Solutions?
BWA Index Referencing Failed. Possible Reason and Solutions? 0 Script: echo “STEP 2: Map to reference using BWA-MEM” #BWA index reference bwa index ${ref} *#Path for ref variable has been defined* #BWA alignment bwa mem -t 4 -R “@RG\tID:SRR062634\tPL:ILLUMINA\tSM:SRR062634” ${ref} ${reads}/SRR062634_1.filt.fastq.gz ${reads}/SRR062634_2.filt.fastq.gz > ${aligned_reads}/SRR062634.paired.sam **Error:** . . . . [BWTIncConstructFromPacked]…
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…
Association of PIK3CA Mutation With Pathologic Complete Response and Outcome by Hormone Receptor Status and Intrinsic Subtype in Early-Stage ERBB2/HER2-Positive Breast Cancer | Oncology | JAMA Network Open
Key Points Question What is the association of PIK3CA mutations, response to therapy, and outcome by hormone receptor (HR) status and intrinsic subtype among patients with ERBB2/HER2-positive early breast cancer (EBC) treated in a clinical trial? Findings In this cohort study of 184 patients enrolled in the phase 3 trial…
My paired end data became single end data after mapping
My paired end data became single end data after mapping 1 Dear community, Something weird happened to me, my public dataset is obviously paired-end data (stated in ‘metadata’ part of ENA database, and there are two seperate fastq files (R1 & R2) and index file (I1) per sequencing run). After…
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…
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.,…
Study uncovers vast genomic diversity in Aboriginal Australian communities
In a recent study published in the journal Nature, researchers investigated the previously underrepresented genomic diversity of four Aboriginal Australian communities. They used population-scale whole-genome (WGS) long-read sequencing. Study findings revealed unique alleles comprised of insertion-deletion variants, variable copy number regions, and structural variants, 62% of which are novel to…
Archaic Introgression Shaped Human Circadian Traits | Genome Biology and Evolution
Abstract When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely, Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultraviolet radiation and increased variation in…
The landscape of genomic structural variation in Indigenous Australians
Cohorts Saliva and/or blood samples were collected from consenting individuals among four NCIG-partnered communities: Tiwi Islands (comprising the Wurrumiyanga, Pirlangimpi and Millikapiti communities), Galiwin’ku, Titjikala and Yarrabah, between 2015 and 2019. Non-Indigenous comparison data, generated from unrelated Australian individuals of European ancestry, was drawn from two existing biomedical research cohorts:…
GetPileupSummaries intervals-list with Targeted Sequencing?
GetPileupSummaries intervals-list with Targeted Sequencing? 0 Hi! I am applying the GetPileUpSummaries, for somatic variant calling starting from targeted sequencing .fasta. I aligned the file with the GrCh38 reference. And currently I am at the GetPileUpSummariesStep. gatk –java-options -Xmx200G GetPileupSummaries \ -I $RECBAM \ -L ???? \ -O $OUTPUT \…
Ambiguous genes due to aligners and their impact on RNA-seq data analysis
Datasets To avoid the so-called ‘dataset bias’20,that some datasets are generated with specific structures and thus the results are ‘over-optimistic’ (in the case of working with our novel method), we performed the analysis in the light of several real datasets (see Table 4). We used four different datasets from the NCBI…
Convert NCBI Downloaded files to ANNOVAR format
Convert NCBI Downloaded files to ANNOVAR format 0 I have been trying to understand from the ANNOVAR documentation and other sites the steps needed to make these files from NCBI available to ANNOVAR. I admit to being new to bioinformatics, but have been a software developer for 30+ years. My…
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…
Where can I get a list of SNPs mapping overlapping genes in humans?
Given files genes.bed and snps.bed, you could do something like: $ bedmap –echo –echo-map-id –delim ‘\t’ genes.bed snps.bed > answer.bed The file answer.bed will contain the gene annotation and a semi-colon delimited list of SNP identifiers that overlap each gene. In order to get genes.bed, you could use Gencode v44…
Help with gatk CreateSequenceDictionary
Help with gatk CreateSequenceDictionary 0 Hi Biostars, I checked my path to the hg38.fa but still don’t know what cause the error. Would you please have a suggestion? Thank you so much. gatk CreateSequenceDictionary R=/variant_calling/Desktop/demo/supporting_files/hg38/hg38.fa O=/variant_calling/Desktop/demo/supporting_fi les/hg38/hg38.dict Invalid argument ‘R=/variant_calling/Desktop/demo/supporting_files/hg38/hg38.fa’ GATK • 39 views Read more here: Source link
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″…
Exome-wide benchmark of difficult-to-sequence regions using short-read next-generation dna sequencing
doi: 10.1093/nar/gkad1140. Online ahead of print. Atsushi Hijikata 1 , Mikita Suyama 2 , Shingo Kikugawa 3 , Ryo Matoba 3 , Takuya Naruto 4 , Yumi Enomoto 4 , Kenji Kurosawa 4 5 , Naoki Harada 6 , Kumiko Yanagi 7 , Tadashi Kaname 7 , Keisuke Miyako 8 , Masaki Takazawa 8 , Hideo Sasai 8 9 , Junichi…
bwa mem hangs after a few thousand reads
I am trying to align a bunch of paired sample fastq files using bwa mem. My original command was: bwa mem -t 8 hg38.fa sample_read1.fq.gz sample_read2.fq.gz > sample_paired.sam I am running this on a HPC cluster. These files have approx. 25 million reads, so I initially anticipated that they might…
Generate Read counts from bam file
Generate Read counts from bam file 2 Currently i am working on a project related to LHON disease (rare mitochondrial disorder which leads to progressive visual loss). I have 9 RNA-seq fastq files out of which 3 are for carriers, 3 for affected and 3 for control. Data downloaded is…
low rate of ‘Successfully assigned alignments’
Hello everybody. I’m a newbie in RNA-seq Analysis, and I have this situation that I don’t really understand. While working with featureCounts for RNA-seq read quantification, I came across an intriguing issue. The rate of successfully assigned alignments turned out to be unexpectedly low, totalling just 15463270 (7.6%). This was…
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…
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…
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,…
issue in RNA -seq analysis
Forum:issue in RNA -seq analysis 0 hello all. i am working on RNA seq analysis. i would like to know following things: first i downloaded genome fasta file for non-coding rna from ensembl and got the gtf file for hg38 from there itself. performed hist2 and got 17% alignment for…
Evaluating 17 methods incorporating biological function with GWAS summary statistics to accelerate discovery demonstrates a tradeoff between high sensitivity and high positive predictive value
Method selection We reviewed the published literature through February 2020 to identify methods that met the following criteria: i. Descriptively categorized as (a) annotation-based; (b) pleiotropy-based; or (c) eQTL-based. ii. Utilized GWAS summary statistics, as opposed to individual-level genotype data. iii. Implemented using freely-available software or packages. iv. Provided either…
selection of reference genome
selection of reference genome 1 hello everyone, I got a vcf file with variation called using hg38 as reference genome. I wonder what would happen if I use hg19 as reference genome to annotate these variants. Would it be OK or get wrong? Thanks! hg19 reference genome hg38 • 25…
Salmon index problem
Salmon index problem 0 Hello, I’m trying to use Salmon in the mapping-based mode, and I downloaded the full decoy salmon indices via refgenie list here using the refgenie command refgenie pull hg38/salmon_sa_index and it download the full folder locally. Now I have this index folder and SRR21898893_1.fastq.gz and SRR21898893_2.fastq.gz…
Allelic hierarchy for USH2A influences auditory and visual phenotypes in South Korean patients
Genotypes of USH2A-related disorders We identified 14 biallelic variants in USH2A, either homozygous or compound heterozygous, in a trans configuration. The segregation of these variants was confirmed by Sanger sequencing. Overall, 18 mutant alleles were implicated in the diagnosis of USH2A-related phenotypes, including c.251G > A:p.Cys84Tyr, c.2209C > T:p.Arg737*, c.2802 T > G:p.Cys934Trp, c.4372C > T:p.Arg1578Cys, c.4858C > T:p.Gln1620*, c.7120 + 1475A > G, c.8232G > C:p.Trp2744Cys,…
BaseRecalibrator takes forever to run. Any suggestions?
BaseRecalibrator takes forever to run. Any suggestions? 1 Hello, I am trying to run BaseRecalibrator tool from GATK package and it takes forever (more than 4 days per one bam file). The command I’m using is: gatk BaseRecalibrator -I NG-01_1_S1_dedup_bwa.bam -R /rumi/shams/genomes/hg38/hg38.fa –known-sites Mills_and_1000G_gold_standard.indels.hg38.vcf.gz –known-sites 1000G_phase1.snps.high_confidence.hg38.vcf.gz –known-sites Homo_sapiens_assembly38.dbsnp138.vcf -O NG-01_1_S1_dedup_bwa_BSQR.table…
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…
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…
Corrupted sam file from bwa. [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped
Corrupted sam file from bwa. [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped 0 I am trying to extract unaligned reads from bam files and then realign them back to hg38. Here are the commands for these steps: samtools view -@ 16 -b -F 2 $bamfile | samtools…
Query regarding callsets used as known sites in Variant Calling
Query regarding callsets used as known sites in Variant Calling 0 Hi, Where can I learn more about the standard VCF files that are used as known sites during the BQSR step in Variant Calling with GATK? The files are: Homo_sapiens_assembly38.dbsnp138.vcf Homo_sapiens_assembly38.known_indels.vcf.gz Mills_and_1000G_gold_standard.indels.hg38.vcf.gz I am aware that these files are…
Clumping with r2=0 and 250kb radius in plink
Clumping with r2=0 and 250kb radius in plink 1 Hi, I am doing clumping with the follow command: plink \ –bfile ${myfilename} \ –keep all_hg38_EUR.ids \ –clump ${trait}_tmp2.txt \ –clump-snp-field SNP \ –clump-field P \ –allow-extra-chr \ –memory 30000 \ –clump-p1 5e-8 \ –clump-r2 0 \ –clump-kb 250 \ –out…
AlphaMissense_hg38.tsv.gz tabix indexing issue VEP
AlphaMissense_hg38.tsv.gz tabix indexing issue VEP 1 Hi! I’m experiencing the issue with the tabix indexing of AlphaMissense_hg38.tsv.gz file. I’ve installed alphamissense plugin in VEP and have downloaded the requested files and launch the tabix command before use it. The error tells me that it can not be indexed directly because…
Inquiry Regarding NA P-values in Logistic Regression
Thank you for your assistance. I apologize for the inconvenience, but I still have a question to ask you. In the output file after conducting logistic regression, I do not see an “ERROR” column. Does this indicate that my data has all passed the multicollinearity check? Additionally, regardless of how…
samtools – Corrupted sam file from bwa. [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped
I am trying to extract unaligned reads from bam files and then realign them back to hg38. Here are the commands for these steps: samtools view -@ 16 -b -F 2 $bamfile | samtools sort -@ 16 -n – | samtools fastq – -1 unaligned.fq1 -2 unaligned.fq2 bwa aln -k…
Diagnosis of Two meningitis Cases caused by Rickettsia felis
Introduction Rickettsia felis belongs to the transitional group in the genus Rickettsia and is mainly transmitted by the cat flea (Ctenocephalides felis) but has been detected in a variety of arthropods including mosquitoes, ticks, and mites.1 Flea-borne spotted fever is caused by R. felis, with symptoms including fever, headache, and…
How To Get Chromosome Position Given Rs Number?
How To Get Chromosome Position Given Rs Number? 3 I have a list of a few hundred SNPs given by rs number. I want to get the chromosome and position for each SNP. For example: input: rs4477212 output: chr1:82154 snp chromosome position • 29k views you can download this information…
ABCB1 and immune genes in breast cancer
Introduction Chemoresistance is a major challenge for breast cancer treatment.1 The mechanisms of chemoresistance are complex because of crosstalk between receptor tyrosine kinases and downstream pathways, deregulation of cell-cycle and apoptosis regulators, and modulation of tumor-infiltrating immune cells.2 The ATP-binding cassette (ABC) superfamily is one of the largest families of…
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…
MELT-SINGLE “priors” list usage
I’m trying to get “priors” working with MELT-SINGLE but nothing I’ve done seems to be making a difference. As a test, I run 1 sample without a priors list java -Xmx6G -jar MELT/MELTv2.2.2.jar Single -bamfile HT-7604-01A-11D-2088.bam -t MELT/me_refs/Hg38/ALU_MELT.zip -h hg38.chrXYM_alts.fa -n MELT/add_bed_files/Hg38/Hg38.genes.bed -w HT-7604-01A-11D-2088-run1/ Command Line:MELT.jar Single -bamfile HT-7604-01A-11D-2088.bam -t…
IJMS | Free Full-Text | CRISPR/Cas9 Directed Reprogramming of iPSC for Accelerated Motor Neuron Differentiation Leads to Dysregulation of Neuronal Fate Patterning and Function
1. Introduction As the world population ages, neurodegenerative diseases are increasing. The outcome of these diagnoses varies but can lead to fatality 50% of the time within 15–20 months [1]. Treatments for neurodegeneration, in particular motor neuron (MN) diseases, are restricted due to the limitations of motor neuron repair and…
Finding exons that are always included
Finding exons that are always included 2 How would I approach the problem of finding hg38 exons that are not affected by alternative splicing/are always included across all cell types? Is there an easier way than looking at percent spliced in from published alternative splicing datasets of many different tissues?…
Powered by PacBio: Selected publications for October 2023
PacBio HiFi sequencing technology continues to play an increasingly pivotal role in advancing critical research across the life sciences. In this blog series, we explore some of the latest and most exciting scientific papers and preprints that demonstrate the power of HiFi sequencing in unraveling new insights in areas as…
Bioconductor – cadd.v1.6.hg38
DOI: 10.18129/B9.bioc.cadd.v1.6.hg38 CADD v1.6 Pathogenicity Scores AnnotationHub Resource Metadata for hg38 Bioconductor version: Release (3.18) Store University of Washington CADD v1.6 hg38 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for University of Washington CADD v1.6 hg38 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to…
Correction of a homoplasmic mitochondrial tRNA mutation in patient-derived iPSCs via a mitochondrial base editor
Human induced pluripotent stem cells (iPSCs) Reprogramming and Culture This study was ethically approved by the Medical Ethics Committee of Nanjing Maternal and Child Health Care Hospital (2021KY-131), and informed consents were obtained from the patient’s legal guardian as well as the healthy donors, in accordance with the Declaration of…
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”) +…
Structural Variants in gnomAD v4
Today, we are thrilled to announce the release of genome-wide structural variants (SVs) for 63,046 unrelated samples with genome sequencing (GS) data. All site-level information for 1,199,117 high-quality SVs discovered in these samples is browsable in the gnomAD browser (gnomAD SV v4) and downloadable from the gnomAD downloads page. For…
Single-nucleus DNA sequencing reveals hidden somatic loss-of-heterozygosity in Cerebral Cavernous Malformations
Ethical statement Our research complies with all relevant ethical regulations, including the Declaration of Helsinki and has been approved by the Institutional Review Boards of University of Chicago, Duke University and the Alliance to Cure Cavernous Malformations. Cerebral cavernous malformation lesions All human CCM tissue specimens have been previously reported18,19…
Failed to download IlluminaHumanMethylationEPICv2anno.20a1.hg38
Failed to download IlluminaHumanMethylationEPICv2anno.20a1.hg38 1 I am currently working on illumina EPIC v1 and v2 data. When trying to annotate the v2 data I am unable to download the annotation package (note: the manifest package works fine). I get the error that the download failed and that ‘rhdf5filters’ is old….
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…
Quickly retrieve reference genome sequence within python
Quickly retrieve reference genome sequence within python 0 Hi all, For a project I’m working on, I need to be able to quickly retrieve the sequence at a given 2kb window of the reference genome hg38 within python. The windows I need might not be consecutive (i.e. one thread might…
Index of /compbio1/eGTEx-H3K27ac/Processed_files/haQTL/gAREandhaQTL_hg38
Name Last modified Size Description Parent Directory – Brain.emp.pvals.hg38.tsv.gz 2022-12-25 15:40 9.8M Brain_allPairs/ 2022-12-28 00:07 – Heart.emp.pvals.hg38.tsv.gz 2022-12-25 15:41 6.8M Heart_allPairs/ 2022-12-28 00:09 – Lung.RSC0.8OrMatched.emp.pvals.hg38.tsv.gz 2022-12-25 15:41 5.1M Lung_allPairs/ 2022-12-28 00:10 – Muscle.emp.pvals.hg38.tsv.gz 2022-12-25 15:41 7.4M Muscle_allPairs/ 2022-12-28 00:09 – …
Bioconductor – AlphaMissense.v2023.hg38
DOI: 10.18129/B9.bioc.AlphaMissense.v2023.hg38 AlphaMissense v2023 Pathogenicity Scores AnnotationHub Resource Metadata for hg38 Bioconductor version: Release (3.18) Store Google DeepMind AlphaMissense v2023 hg38 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for Google DeepMind AlphaMissense v2023 hg38 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those…
DNA-binding protein PfAP2-P regulates parasite pathogenesis during malaria parasite blood stages
Parasite culture, maintenance, synchronization and transfection The DiCre-expressing P. falciparum clone II3 (ref. 10) was maintained in human A+ erythrocytes at 37 °C in Roswell Park Memorial Institute 1640 medium containing AlbumaxII (Invitrogen) supplemented with 2 mM l-glutamine. Parasites were either synchronized by sorbitol treatment or by purifying mature schizont stages using…
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…
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 =…
Problems when running GDC_prepare in R
Problems when running GDC_prepare in R 0 @2158037f Last seen 3 hours ago Macao Enter the body of text here Code should be placed in three backticks as shown below library(TCGAbiolinks) query <- GDCquery( project = “TCGA-LIHC”, data.category = “Transcriptome Profiling”, data.type = “Gene Expression Quantification”, workflow.type = “STAR -…
Solved bedtools getfasta -s -fi \$dataCommon/hg38.fa -bed
Transcribed image text: bedtools getfasta -s -fi \$dataCommon/hg38.fa -bed test.bed -fo test.bed.fa bedtools getfasta -fi \$dataCommon/hg38.fa -bed test.bed -fo test.bed.2.fa \# promoter [−5,0] in srand specific manner; ONLY UPSTREAM PROMOTER SELECTION IS POSSIBLE bedtools flank -i test.bed -g \$dataCommon/hg38.chrom.sizes.txt -I 5 -r 0 -s Highlight Both regions having…
No valid chromosomes found! on Michigan Imputation Server
I have two vcf files – one hg19 and one hg38, analysing data from the same participants on two slightly different SNP platforms. Both files have been through the pre-imputation checks. The header (and the first line) of the hg38 version looks like: ##fileformat=VCFv4.3 ##FILTER=<ID=PASS,Description=”All filters passed”> ##fileDate=20230906 ##source=PLINKv2.00 ##contig=<ID=chr1,length=248917420>…
Cannot find summary message after Bowtie2 mapping
Cannot find summary message after Bowtie2 mapping 0 Hi all, I tried to align the reads in Bowtie2 and command the a SAM file output. I also expect a summary file to be saved as output file. But I can only find the SAM file. did I miss out any…
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…
Pre-imputation checks using 1000G data (hg19) for a hg38 VCF
Pre-imputation checks using 1000G data (hg19) for a hg38 VCF 0 I’m trying to use the pre-imputation checks here www.well.ox.ac.uk/~wrayner/tools/ to check a vcf (on the hg38 assembly) on the 1000G phase 3 v5 data, which is hg19, before imputing using the MIS. Obviously, very few of the variants in…
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…
map Ensembl gene ID from hg19 to hg38
map Ensembl gene ID from hg19 to hg38 0 Hello! I would like to convert Ensembl gene ID from hg19 to hg38 with R. I tried with this code: ensembl <- useMart(“ensembl”, dataset = “hsapiens_gene_ensembl”, host= “grch37.ensembl.org“) ensembl_ids <- c(“ENSG00000183878”, “ENSG00000146083”) converted_ids <- getLDS(attributes = c(“ensembl_gene_id”), filters = “ensembl_gene_id”, values…
Apoptotic stress causes mtDNA release during senescence and drives the SASP
Cell culture and treatments Human embryonic lung MRC5 fibroblasts (ATCC) and IMR90 fibroblasts (ATCC) were grown in Dulbecco’s modified Eagle’s medium (Sigma-Aldrich, D5796) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 100 U ml−1 penicillin, 100 μg ml−1 streptomycin and 2 mM l-glutamine and maintained at 37 °C under 5% CO2. MRC5 fibroblasts were cultured in…
ROSE Algorithm: index out of range
Hi again, I am trying to run the ROSE algorithm created by the young lab, url here: younglab.wi.mit.edu/super_enhancer_code.html Specifically, I am running the ROSE_main.py script: younglab.wi.mit.edu/super_enhancer_code.html I created a python 2.7 environment to run the script as it is compatible with python 2.7. When I run the script in ubuntu:…
Genotyping, sequencing and analysis of 140,000 adults from Mexico City
Recruitment of study participants The MCPS was established in the late 1990s following discussions between Mexican scientists at the National Autonomous University of Mexico (UNAM) and British scientists at the University of Oxford about how best to measure the changing health effects of tobacco in Mexico. These discussions evolved into…
Solved 1. Download fastq files using the command below, and
Transcribed image text: 1. Download fastq files using the command below, and answer the questions: fastq-dump -X 1000 –split-files SRR12544599 1.1 Run fastQC on the two fastq files: SRR12544599_1.fastq and SRR12544599_2.fastq. Upload the report (just the .html files) that was generated by running fastqc. 1.2 Was there warnings reported in…
1. Download fastq files using the command below, and
Transcribed image text: 1. Download fastq files using the command below, and answer the questions: fastq-dump -X 1000 –split-files SRR12544599 1.1 Run fastQC on the two fastq files: SRR12544599_1.fastq and SRR12544599_2.fastq. Upload the report (just the .html files) that was generated by running fastqc. 1.2 Was there warnings reported in…
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…
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…
hisat2 index file error
hisat2 index file error 1 hi dear i do hisat2 -q -x ../hg38/*.ht2 -1 SRR23132814_1_trim.fastq -2 SRR23132814_2_trim.fastq –add-chrname -S SRR23132814.sa and also i do hisat2 -q -x //wsl.localhost/Ubuntu-22.04/home/alikian/RNAseqData/hg38/*.ht2 -1 SRR23132814_1_trim.fastq -2 SRR23132814_2_trim.fastq –add-chrname -S SRR23132814.sa but i see this error (ERR): “../hg38/genome.1.ht2” does not exist Exiting now … or this…
The Therapeutic Effects of MUC1-C shRNA@Fe3O4 Magnetic Nanoparticles i
Introduction Breast cancer (BC) is a malignant tumor originating from the epithelial tissue of the breast and is the most common malignancy in women.1 It is estimated that by 2040, there will be 3,000,000 new cases of BC and 100,000 deaths worldwide. Triple-negative breast cancer (TNBC), which accounts for 15–20%…
How to choose LiftOver chain file
How to choose LiftOver chain file 1 I am trying to liftover a hg38 Whole Genome Sequenced VCF to hg19 VCF. Planning to use GATK Picard for this. However not sure which liftover chain file to use from this path: hg38tohg19 picard LiftOver • 32 views • link updated 31…
Help with error velocyto
Help with error velocyto 0 Hi Biostars, I try to get the loom file and after trying I still don’t know how to fix this error: velocyto run -b MT/outs/filtered_feature_bc_matrix/barcodes.tsv -o output_dir -m Hg38_rmsk.gtf MT/outs/possorted_genome_bam.bam /cellranger/reference/refdata-cellranger-GRCh38 -3.0.0/genes/genes.gtf –samtools-memory 8000 –samtools-threads 8 MemoryError: bam file #0 could not be sorted by…
Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer’s disease brains | Cell & Bioscience
Lo MT, Kauppi K, Fan CC, Sanyal N, Reas ET, Sundar VS, Lee WC, Desikan RS, McEvoy LK, Chen CH, Alzheimer’s Disease Genetics, C. Identification of genetic heterogeneity of Alzheimer’s disease across age. Neurobiol Aging. 2019;84(243):e241-243. doi.org/10.1016/j.neurobiolaging.2019.02.022. Article Google Scholar Nacmias B, Bagnoli S, Piaceri I, Sorbi S. Genetic heterogeneity…
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”…
Help with error running velocyto
Help with error running velocyto 1 Hi Biostars, I try to get the loom file to do velocity analysis: velocyto run10x -m Hg38_rmsk.gtf WT/outs /cellranger/reference/refdata-cellranger-GRCh38-3.0.0/genes/genes.gtf Inside WT/outs I have some folders such as filtered_feature_bc_matrix. Inside filtered_feature_bc_matrix, I have barcodes.tsv.gz ERROR – This is an older version of cellranger, cannot check…
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…
HG38 / GRCh38 Human Y Chromosome hg38/GRCh38: 101 bp from chrY:14,000,000..14,000,100
International Society of Genetic GenealogyISOGG YBrowseHuman Y Chromosome Pangenome Browser ISOGGResourcesYSNP-TreeSpeakers ListMeetings/EventsYbrowse Raw Data File Bookmark this Share these tracks Export as… …low-res PNG image …editable SVG image …GFF annotation table …FASTA sequence file Get chrom sizes Reset to defaults Help Help with this browser About GBrowse… About this database……
Is SeqSQC compatible with hg38?
Is SeqSQC compatible with hg38? 1 @d0d83382 Last seen 8 hours ago Switzerland Dear Bioconductor team, I am contacting you because for my PhD project we have done whole genome sequencing with 30x coverage of 50 patients. We got the fastq files from the sequencing facility and now I am…
QC of genetic data
QC of genetic data 0 Hi, I have some genetic data in a bim file. The chromosomes range from 0 to 23 and 26, which I have not come across before. Would the SNPs on chromosome 0 and 26 be removed from the genetic file or left in. Then, I…
TRIM25 targets p300 for degradation
Introduction Protein levels are regulated at several nodes. One mode of protein level regulation acts through enhancing or reducing gene transcription. Gene transcription can be stimulated by binding transcription factors to promoters or enhancers of target genes and by posttranslational modifications of transcription factors and histones. Such modifications can be…
Chip-Seq and correlation of bam file
Chip-Seq and correlation of bam file 1 I want to compare replicates, I calculated read counts over each bin (5 kilobases (kb)) across the whole genome using these commands: bedtools makewindows -g hg38.fa.txt -w 5000 >hg38.5Kb.windows.bed bedtools intersect -a hg38.5Kb.windows.bed -b sample1.sorted.bam -c -sorted >sample1.5Kb.windows.counts.bedg Now, I want to calculate…
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…
filtering variants in a Strelka2 VCF file based on AD and AF
Dear all, I would appreciate having your suggestions on the following. I am working with a VCF file that was produced by Strelka on Tumor-Normal pairs. As it is well known, Strelka2 does not provide Allele Depth (AD) or VAF (variant allele fraction) in the VCF fields. I have used…
Using STAR aligner to build index of hg38
Using STAR aligner to build index of hg38 0 Hi, I’m using STAR aligner to build index, and I want to use hg38 as reference genome. But I think hg38 is DNA level. Can it also be used as a reference genome for RNAseq? (My data is RNAseq) hg38 STAR…
capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements
Cell culture All cell lines were grown in 6 cm dishes at 37 °C in a 5% CO2 incubator. The K562, MDA-MB-231 and HCT 116 cell lines were cultured in high-glucose DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin antibiotics (pen-strep). NCM460 cells were cultured in RPMI 1640 medium supplemented…
Troubleshooting BWA-MEM2 resources under Docker Galaxy – mapping
Hi Jenna,I ran into this same error.With fastp cleaned data, I can use bwa-mem2 to run a dataset to 1 or 2 genes of the reference hg38. I then tried running the 48 pairs in the collection against the single gene. That works. but when I scaled to the complete…
What is the difference between norm –multiallelics -any versus –atomize?
What is the difference between norm –multiallelics -any versus –atomize? 1 Hello, forgive my ignorance- Suppose input.vcf contains a complex multiallelic site. What is the difference between bcftools norm –multiallelics -any -f hg38.fa input.vcf versus bcftools norm –atomize -f hg38.fa input.vcf I understand what –multiallelics -any does but not sure…
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…
FGC21024 – YFull YTree Info
R-FGC21024 – YFull YTree Info SNPs currently defining R-FGC21024 FGC85126 FGC20988 V5770 / FGC21024 Sample ID Country / Language Info Ref File Testing company Statistics Status YF075661 —— R-FGC20980* —— Hg38 .BAM FTDNA (Y700) 41X, 18.7 Mbp, 151 bp HG01947 new —— R-Y34349 HG01947_old T2T .BAM Scientific…
YP311 – YFull YTree Info
Sample ID Country / Language Info Ref File Testing company Statistics Status YF122695 new Austria (Oberösterreich) / German R-YP311* —— T2T .BAM Nebula Genomics 17X, 45.1 Mbp, 150 bp YF067341 Russia (Chuvashskaya Respublika) / Chuvash R-YP311* —— Hg19 .BAM Dante Labs 13X, 23.0 Mbp, 151 bp YF016502 Italy (Palermo) R-YP311*…
hg38 1kg/GATK is not available in the Lift Genome Annotation tool
Manuel Dominguez Clinical Bioinformatician (trainee) Wessex Genomics Laboratory Service (Salisbury) Salisbury District Hospital, Salisbury, SP2 8BJ. UK Tel (direct line) 01722 336262 (ext 3704) Tel (admin office) 01722 429080 www.wrgl.org.uk Please note…
Is a PON necessary for tumor-normal matched Mutect2?
Is a PON necessary for tumor-normal matched Mutect2? 1 I’m a bit confused on whether or not i should include GATK’s public PON (either 1000g_pon.hg38.vcf.gz since I aligned with hg38), make my own from my normal samples, or just leave it and not include a PON. I am planning on…