Tag: BED

The necessity of ultrapure water in cell culture

Sponsored Content by SartoriusJun 30 2022Reviewed by Alex Smith When experimenting with cell cultures, contaminants in water can come in a number of different types, such as yeasts, molds or bacteria. Typically, these contaminants can be observed using optical microscopy or by the eye. Contamination from alternative biological agents or…

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extendedSequences length is not the required for DeepCpf1 (34bp)

Hi, I’m using CRISPRseek dev v. 1.35.2, installed from github (hukai916/CRISPRseek). I wanted to calculate the CFD, and the grna efficacy of a Cas12 sgRNA (my_sgrna.fa file) using Deep Cpf1. my_sgrna.fa, TTTT (PAM) + sgRNA (20bp): >sgrna1 TTTTTGTCTTTAGACTATAAGTGC Command: offTargetAnalysis(inputFilePath = “my_sgrna.fa”, format = “fasta”, header = FALSE, exportAllgRNAs =…

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Beam Therapeutics Stock: A Leader in Gene Editing Tech?

Don’t invest in stories. Don’t invest in a company before they have meaningful revenues. Don’t invest in drug developers that have a great deal of regulatory risk. These are all rules we need to break if we want exposure to a technology that allows mankind to start playing with the…

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Genome-wide association study of musical beat synchronization demonstrates high polygenicity

Savage, P. E., Brown, S., Sakai, E. & Currie, T. E. Statistical universals reveal the structures and functions of human music. Proc. Natl Acad. Sci. USA 112, 8987–8992 (2015). CAS  PubMed  PubMed Central  Article  Google Scholar  Ravignani, A., Delgado, T. & Kirby, S. Musical evolution in the lab exhibits rhythmic…

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SMARCE1 deficiency generates a targetable mSWI/SNF dependency in clear cell meningioma

Clapier, C. R., Iwasa, J., Cairns, B. R. & Peterson, C. L. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat. Rev. Mol. Cell Biol. 18, 407–422 (2017). CAS  PubMed  PubMed Central  Article  Google Scholar  Mashtalir, N. et al. Modular organization and assembly of SWI/SNF family chromatin remodeling complexes….

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Genome hg19**not found in homer config

I want to use the Homer to do annotation. After I input “annotatePeaks.pl 31512_TH0_D0.bed hg19 > 31512_TH0_D0.ann.txt” , it shows “!!!!Genome hg19 not found in /home/jenny/NGStools/homer/.//config.txt” I used the command “perl /home/jenny/NGStools/homer/configureHomer.pl -install hg19” to install it, and I am sure I installed the hg19 for the homer Then input…

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a strange pattern of repetitive summits

Problem with the output of Deeptools PlotProfile: a strange pattern of repetitive summits 0 Hi! I am trying to plot DNA binding profiles of my ChIP-seq bw files using Deeptools plotProfile. I generated the matrix using the computeMatrix reference-point. I used some publicly available bed files as my regions of…

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Standard for aligning smallRNA to a reference human rRNA?

Standard for aligning smallRNA to a reference human rRNA? 0 Hi, I need to label some smallRNA sequences that I know are rRNA fragments. I know that for mRNA these are discarded by aligning to the human genome and filtering out multimapped reads, but I need to try to pin…

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Bcftools equivalent of vcftools conversion to ped & map

Bcftools equivalent of vcftools conversion to ped & map 1 I am converting a VCF to ped & map thus in vcftools vcftools –gzvcf ZZZZZTYT.vcf.gz –plink –out ZZZZZTYT which works fine. However, I have been searching and searching, can bcftools do the same with a bcf? bcftools • 103 views…

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bedtools interset doesn’t return a VCF file?

bedtools interset doesn’t return a VCF file? 1 I am filtering a VCF file with a bed file using Bedtools. I have carried out this successfully with bedtools intersect -wb -a myVCF.vcf -b myBEDfile.bed > output.txt However, what I want is to get a VCF file with the metadata and…

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Why so much variability in RNA-seq technical replicates?

Why so much variability in RNA-seq technical replicates? 1 Hi all, I download an RNA seq data for gene expression analysis from NCBI. When I did counts with bedtools for my gene of interest, the variability was too much. Does that mean this data is unreliable? What could have caused…

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Extact SNPs ID’s and their Values with IID, Additive and dominance components

Extact SNPs ID’s and their Values with IID, Additive and dominance components 0 I’m dealing with GWAS data and I have 2M records of the .bed file, I’m New to P-link, Can anyone please help me with the Plink command which can Extract all SNPs Id’s and their Values with…

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Calculate scores using certain method by comparing a bedGraph file from treatment and a file from control representing local bias

bdgcmp(1) Calculate scores using certain method by comparing a bedGraph file from treatment and a file from control representing local bias SYNOPSIS bdgcmp <-t TREATMENT.BEDGRAPH> <-c CONTROL.BEDGRAPH> <-o OUTPUT.BEDGRAPH> [-m METHOD] DESCRIPTION Calculate scores using certain method by comparing a bedGraph file from treatment and a file from control representing…

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Building custom hg38 – alt contigs

I am exploring modifications of hg38 like these: github.com/mebbert/Dark_and_Camouflaged_genes Starting from the regular bcbio hg38 data installation Masking hg38.fa using bedtools maskfasta Generating indexes using bcbio_setup_genome.py for seq and bwa as described in the manual The bwa directory then contains ├── bwa │   ├── hg38_masked.fa.amb │   ├── hg38_masked.fa.ann │   ├──…

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Keep IUC Galaxy bedtools tool wrappers in sync with the command line bedtools releases

For example, as of the time of the writing, IUC Galaxy bedtools still uses only the command line options available in the release v2.28.0 (Mar 23, 2019): github.com/galaxyproject/tools-iuc/commit/2962180c31dea5883b2ee529fe26b51c4dbc4d36 But the main (this) bedtools repo has already the release v2.29.2 (Dec 17, 2019): github.com/arq5x/bedtools2/releases/tag/v2.29.2 IUC Galaxy bedtools are widely used. It…

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Voxel Printing Anatomy: Design and Fabrication of Realistic, Presurgical Planning Models through Bitmap Printing

This method demonstrates a voxel-based 3D printing workflow, which prints directly from medical images with exact spatial fidelity and spatial/contrast resolution. This enables the precise, graduated control of material distributions through morphologically complex, graduated materials correlated to radiodensity without loss or alteration of data. Bitmap printing allows for the direct…

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deeptools plotHeatMap – Convert bed files to gene list?

I might suggest limiting your search to genes: gtf2bed < Mus_musculus.GRCm38.102.gtf | grep -w “gene” > sorted-mm10.genes.bed But that’s up to you. Otherwise, I think you may also get transcripts/exons, which may be more than you want. Again, up to you. If hnf4a-ko-downreg-clusters.bed is the file containing peaks, as described…

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Convert bedGraph to Homer tag directory?

Convert bedGraph to Homer tag directory? 0 Hi, I am new to ChIP-seq analysis. When taking published data in .bedGraph format (generated by Homer), is there any way to convert back to Homer tag directory? (other than aligning from the raw .fasta). I suppose extracting columns into .bed format and…

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Merge only bim files with plink

Merge only bim files with plink 0 Hello For the same dataset they provide a single BED and FAM files for all the chromosomes. However, the BIM files are split in chromosomes. I would like to generate the VCF file with the genotyping calls of all chromosomes but I need…

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Measurement of Protein Import Capacity of Skeletal Muscle Mitochondria

Mitochondria are key metabolic organelles that exhibit a high level of phenotypic plasticity in skeletal muscle. The import of proteins from the cytosol is a critical pathway for organelle biogenesis, essential for the expansion of the reticulum and the maintenance of mitochondrial function. Therefore, protein import serves as a barometer…

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A genome-scale screen for synthetic drivers of T cell proliferation

Abramson, J. S. et al. Transcend NHL 001: immunotherapy with the CD19-directed CAR T-cell product JCAR017 results in high complete response rates in relapsed or refractory B-cell non-Hodgkin lymphoma. Blood 128, 4192–4192 (2016). Google Scholar  Shifrut, E. et al. Genome-wide CRISPR screens in primary human T cells reveal key regulators…

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Elite sleepers: are you one of the people genetically programmed to need less sleep? | Sleep

Name: Elite sleepers. Age: As old as humanity. Appearance: Currently even smugger than usual. Oh God, what now? This is a time for wild celebration! Science has just proved that so-called “elite sleepers” are less likely to develop dementia. I’m an elite sleeper, in that I never get out of…

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Ubuntu Manpage: sambamba-view – tool for extracting information from SAM/BAM files

Provided by: sambamba_0.8.2+dfsg-2_amd64 NAME sambamba-view – tool for extracting information from SAM/BAM files SYNOPSIS sambamba view OPTIONS <input.bam | input.sam> [region1 […]] DESCRIPTION sambamba view allows to efficiently filter SAM/BAM files for alignments satisfying various conditions, as well as access its SAM header and information about reference sequences. In order…

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bedtools -u not giving unique files

bedtools -u not giving unique files 1 The following are the steps Im following: First step to extract sample using bed file is this (here the bedfile is input bedfile converted to Hg38): tabix -h -R Hg19_to_Hg38_sorted.bed.gz gnomad.genomes.v{g_version}.hgdp_tgp.chr{chr}.vcf.bgz | perl {vcftools} -c {sample_name} > {sample_name}_out.vcf’ output({sample_name}_out.vcf’) chr2 113982416 rs56177103 TATAAAATAAAATAAA…

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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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bam – Detect mutation context in a read of a sam file

That kind of custom fiddling with reads and variants is very cumbersome, non-standard and also error-prone. Do a standard variant callign pipeline and then filter for the mutations that you want. Then extract the variant position (so the coordinates) and get the variant context from the reference genome. Using individual…

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split gtex genotype data by chromosomes.

Hello, I used and edited the command line to use –vcf to import vcf file. I used these commands: for chr in $(seq 1 22); do      plink –vcf /dbGAP/GTEx_Analysis_2017-06-05_v8_WholeExomeSeq_979Indiv_VEP_annot.vcf.gz            –chr $chr            –recode            –out…

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Prediction of histone post-translational modification patterns based on nascent transcription data

Allfrey, V. G., Faulkner, R. & Mirsky, A. E. Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc. Natl Acad. Sci. USA 51, 786–794 (1964). CAS  PubMed  PubMed Central  Google Scholar  Ho, J. W. K. et al. Comparative analysis of metazoan chromatin organization….

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Understanding the number of intersection in bedtools jaccard

Understanding the number of intersection in bedtools jaccard 1 Hello, I am using bedtools jaccard to compare two vcf files, as: bedtools jaccard -a ancestors.calls.norm.snp.vcf.gz -b GC078310.calls.norm.snp.vcf.gz intersection union-intersection jaccard n_intersections 1606899 1806667 0.889427 1536700 What I do not get is why n_intersections is equal to 1536700. Especially, the difference…

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Identification of Hub Genes Associated with COPD Through Integrated Bi

Introduction Chronic obstructive pulmonary disease (COPD) will become the third leading cause of death worldwide.1,2 The incidence of COPD worldwide is 13.1%3 and is 13.7% in the Chinese population over 40 years of age.4 Emphysema is one of the most common phenotypes.1 Over the past few decades, we have conducted…

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bedtools sample with fastq input and fewer input records than requested

I’m using bedtools sample to sample reads from fastq files. I’d like to submit two feature requests: If the number of requested records is larger than the input I get ERROR: Input file has fewer records than the requested number of output records. I guess this is intentional and not…

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Genomic variation from an extinct species is retained in the extant radiation following speciation reversal

Vamosi, J. C., Magallon, S., Mayrose, I., Otto, S. P. & Sauquet, H. Macroevolutionary patterns of flowering plant speciation and extinction. Annu. Rev. Plant Biol. 69, 685–706 (2018). CAS  PubMed  Google Scholar  Rhymer, J. M. & Simberloff, D. Extinction by hybridization and introgression. Annu. Rev. Ecol. Syst. 27, 83–109 (1996)….

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nf-core/circrna

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data Introduction nf-core/circrna is a best-practice analysis pipeline for the quantification, miRNA target prediction and differential expression analysis of circular RNAs in paired-end RNA sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across…

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Butterfly eyespots evolved via cooption of an ancestral gene-regulatory network that also patterns antennae, legs, and wings

Although the hypothesis of gene-regulatory network (GRN) cooption is a plausible model to explain the origin of morphological novelties (1), there has been limited empirical evidence to show that this mechanism led to the origin of any novel trait. Several hypotheses have been proposed for the origin of butterfly eyespots,…

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Genomic analysis on Galaxy using Azure CycleCloud

Cloud computing and digital transformation have been powerful enablers for genomics. Genomics is expected to be an exabase-scale big data domain by 2025, posing data acquisition and storage challenges on par with other major generators of big data. Embracing digital transformation offers a practically limitless ability to meet the genomic…

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Trouble with bedtools getfasta

Trouble with bedtools getfasta 0 I am trying to extract sequences from a .fasta file based on a bed file using bedtools getfasta and I am getting the following error. The command run was the following: bedtools getfasta -fi genomic.fasta -bed bedfile.bed -fo output.fasta WARNING. chromosome (chr1) was not found…

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Find Transposon Element insertions using long reads (nanopore), by alignment directly. (minimap2)

find_te_ins is designed to find Transposon Element (TE) insertions using long reads (nanopore), by alignment directly. (minimap2) Install $ git clone github.com/bakerwm/find_te_ins.git&#13; $ cd find_te_ins Change the following variables upon your condition: genome_fa and te_fa in line-10 and line-11; $ bash run_pipe.sh run_pipe.sh Prerequisite minimap2 – 2.17-r974-dirty, align long…

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Bioconductor on Microsoft Azure – Microsoft Tech Community

Co-authored by: Nitesh Turaga – Scientist at Dana Farber/Harvard, Bioconductor Core Team Erdal Cosgun – Sr. Data Scientist at Microsoft Biomedical Platforms and Genomics team Vincent Carey – Professor at Harvard Medical School, Bioconductor Core Team   Introduction   The Bioconductor project promotes the statistical analysis and comprehension of current and emerging…

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Surgical Techniques to Optimize Ovarian Reserve during Laparoscopic Cystectomy for Ovarian Endometrioma

This protocol presents techniques to laparoscopically excise ovarian endometrioma, to perform adhesiolysis with sparing electrosurgical application, and to employ intraoperative chromopertubation to assess for genital tract patency. This systematic approach will facilitate optimal endometriosis management, guide concomitant adnexal surgeries, and enhance post-surgical fertility outcomes. Surgical techniques to optimize ovarian reserve…

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Efficiently merge two BAM files while retaining reads from only one file in overlapping regions

Efficiently merge two BAM files while retaining reads from only one file in overlapping regions 1 I have a WGS BAM file that is fairly large (>150GB) and a smaller BAM file (<5GB) with reads in a small 10Mbp region. I want to (efficiently) merge the two BAM files while…

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organizing a Bed file for bedtools getfasta

organizing a Bed file for bedtools getfasta 0 I am trying to use bedtools getfasta on some bed files, but the issue is that the peaks bed file columns are mixed up such that the first column with the chromosome names contains the peak location as well for some of…

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Plotting date intervals in ggplot2

I have a dataset which has a bunch of date intervals (i.e. POSIXct format start dates and end dates). In the example provided, let’s say it’s each period is associated to when someone was in school or out of school. I’m interested in plotting the data in ggplot2, each row…

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Convert DNAStringSet to a list of elements in R? (Error in seq[[1]][[“seq”]] : subscript out of bounds in R)

I have a bed file which contains DNA sequences information as follow: ** track name=”194″ description=”194 methylation (sites)” color=0,60,120 useScore=1 chr1 15864 15866 FALSE 894 + chr1 534241 534243 FALSE 921 – chr1 710096 710098 FALSE 729 + chr1 714176 714178 FALSE 12 – chr1 720864 720866 FALSE 988 -…

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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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Bioconda faststructure – gitmetadata

I am using the conda env of faststructure from bioconda channel. Got this error messages. Could it be that the bioconda package needs to be updated? Best regards: python structure.py structure.py:3: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 import fastStructure structure.py:4: RuntimeWarning: numpy.dtype size changed,…

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processing in strelka2 with multiples bam file in directory

processing in strelka2 with multiples bam file in directory 0 If I manually tell strelka2 to use these three bam files below, then I get the desired results of 3 individually genome files in results/variants. xxx_00.bam yyy_01.bam zzz_02.bam ${path_to_strelka}/bin/configureStrelkaGermlineWorkflow.py –bam xxx_00.bam –bam yyy_01.bam –bam zzz_02 –referenceFasta <fasta> –callRegions <.bed.gz> –runDir…

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Getting peak heights from TF chIP-seq data (wig file)

Getting peak heights from TF chIP-seq data (wig file) 1 Hello everyone, I have TF ChIP seq data from NCBI GEO in wig format. I converted wig to bedgraph and then used MACS peak caller to get bed narrowpeak files.I further uploaded file on genome browser to get graphical map…

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Regions File Format – ANGSD-wrapper/angsd-wrapper Wiki

ANGSD-wrapper prefers the regions file to be formatted as chr_name:start_position-end_position. Below, we will create a toy BED file as an example and show how we can go from BED file format to ANGSD-wrapper’s regions file format. Create toy BED file Let’s create an example BED file. You can run the…

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bedtools intersect error: Invalid record in file

Hello to all I am trying to run bedtools intersect with vcf file and a bed file (my goal is to add the depth data to my VCF) I get an error running this command: bedtools intersect -a depth.bed -b fish.vcf -wa -wb > $out The error: “Error: Invalid record…

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What is RNAcentral? | RNAcentral

RNAcentral is a database of non-coding RNA sequences that aggregates ncRNA data from over 40 member resources known as Expert Databases.1 Non-coding RNAs Similar to mRNAs, non-coding RNAs (ncRNAs) are transcribed from DNA but are not translated into proteins. NcRNAs are found in all organisms and have a broad range…

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bedtools genomecov problem with merged bam

Hi, I was using puge haplotig, and in that work flow the first step was to use bedtools genomecov so I moved here. I have three paired end dataset, illumina wgs reads, HiC reads, and Chicago sequencing reads. I aligned the paired end reads of illumina wgs to the genome,…

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How to convert bedgraph file with bins into GRanges object?

You could convert your bedGraph bins from hg18 to hg19 using liftover, so you can overlap them with your peaks. You would read them into a GRanges object, then hand this to the liftover function to translate from hg18 to hg19, then unlist the results to get back a regular…

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Systems biology analysis of human genomes points to key pathways conferring spina bifida risk

Significance Genetic investigations of most structural birth defects, including spina bifida (SB), congenital heart disease, and craniofacial anomalies, have been underpowered for genome-wide association studies because of their rarity, genetic heterogeneity, incomplete penetrance, and environmental influences. Our systems biology strategy to investigate SB predisposition controls for population stratification and avoids…

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P-value cut-off to identify SNPs at ChIP-seq peaks? [BedTools]

P-value cut-off to identify SNPs at ChIP-seq peaks? [BedTools] 0 Hi all, I have a bed file of SNPs and also H3K27ac ChIP-seq .broadpeak file from Roadmap epigenome… I want to find the SNPs in my list that intersects a H3K27ac peak using BedTools intersect However, should I filter the…

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Reference panel data to be used for GCTA-COJO

Reference panel data to be used for GCTA-COJO 0 I performed a genome-wide meta-analysis based on summary statistics from the four cohorts to identify significant loci. Next, I would like to perform a conditional analysis using GCTA-COJO to search for SNPs independent of significant lead SNPs. I know that GCTA…

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Arrange the size of subplots in plotHeatmap deeptools figure

Arrange the size of subplots in plotHeatmap deeptools figure 1 Hi all, I am trying to generate a 10×10 (10 bw files + 10 bed files) figure using deeptools but I am having trouble arranging the size of subfigures. I want the subfigures in the same size but if I…

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computeMatrix in deeptool is Running with no result

computeMatrix in deeptool is Running with no result 0 Hi All, I wonder if someone can help me in explaining what to input on the -R <bed file> argument of the code below? computeMatrix scale-regions -S <bigwig file(s)> -R <bed file> -b 1000 what I did for example, I download…

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A matrix sample for Profile plots and heatmaps of Computematrix, deepTools

A matrix sample for Profile plots and heatmaps of Computematrix, deepTools 0 Hi everyone, I have a count matrix from feature counts and of course, couple of peak (.bed) files. I want to visualize the peaks all together to show the coverage and overall comparing. I was going to use…

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Using STAR SJ.out.tab file to identify novel ncRNAs

Using STAR SJ.out.tab file to identify novel ncRNAs 0 Hi All, I am attempting to identify novel ncRNAs from a circadian RNAseq dataset. Specifically I have a ribo-depleted RNAseq timecourse with 31 samples (sample every 2 hours for 60hrs). I have run STAR (code below). I am trying to follow…

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Piranha Peak-Calling with multiple replicates

Piranha Peak-Calling with multiple replicates 0 I am trying to call RNA-Protein interation peaks by using Piranha software. I have multiple replicates for each experiment and the control data, and I can’t seem to understand how to combine them into one Piranha query. For example, if I was to call…

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PLINK sanity check – Bioinformatics Stack Exchange

I am a new user of PLINK and am analysing some SNP data for the first time. After creating a .bim file with $ plink –file my_data –make-bed I notice that for several SNPs my data is different from dbSNP e.g. rs145496306: BIM file: A G dbSNP: G>A,T rs3813199: BIM…

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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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how to add reference alleles to VCF?

how to add reference alleles to VCF? 1 I’m converting gVCFs to VCF, but the reference alleles are missing. An example below: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 180525_FD02929177 1 97547947 . T . . . DP=31 GT:DP:RGQ 0/0:31:81 1 97915614 . C . . . DP=40…

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SNP extraction

SNP extraction 0 I want to extract specific SNPs of interest i have in a text file into an additive genetics model so that each SNP can be in a 0/1/2 format for each subject using genetics info in from PLINK (.bed, .bim, and .fam files). How can i do…

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Senior Bioinformatics Scientist II/ Staff Bioinformatics Scientist

Inscripta was founded in 2015 and recently launched the world’s first benchtop Digital Genome Engineering platform. The company is growing aggressively, investing in its leadership, team, and technology with a recent $150mm financing round led by Fidelity and TRowe price. The company’s advanced CRISPR-based platform, consisting of an instrument, reagents,…

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bedops bedmap operation in python

bedops bedmap operation in python 1 I noticed there is a conda version of bedops bedmap function available. I’ve been struggling to use it though. Could someone refer me to any documentation of it’s usage in a python script please. Have a great day. Thanks in advance. python bedops bedmap…

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How to call LOH with FreeC

How to call LOH with FreeC 0 Good morning, I am try to infer loss of heterozygosity (LOH) from WGS data using Freec. For this purpose, I am using these parameters in the “[BAF]” section of the configuration file: [BAF] makePileup = My_somaticVCF.vcf.gz fastaFile = hg19.fa SNPfile = hg19_snp142.SingleDiNucl.1based.txt.gz When…

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How To Write Data In A Granges Object To A Bed File.

Given a GRanges object: gr <- GRanges(seqnames = Rle(c(“chr1”, “chr2”, “chr1”, “chr3”), c(1, 3, 2, 4)), ranges = IRanges(1:10, end = 7:16, names = head(letters, 10)), strand = Rle(strand(c(“-“, “+”, “*”, “+”, “-“)), c(1, 2, 2, 3, 2))) You can simply: df <- data.frame(seqnames=seqnames(gr), starts=start(gr)-1, ends=end(gr), names=c(rep(“.”, length(gr))), scores=c(rep(“.”, length(gr))),…

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Intersecting Roadmap’s Histone ChIP-seq data using BedTools?!?!??!

Intersecting Roadmap’s Histone ChIP-seq data using BedTools?!?!??! 0 Hi all, I want to prioritise my list of 112 SNPs by looking at those that lie within open chromatin regions and/or active promoter/enhancer histone marks In order to do that I have downloaded several Histone modification ChIP-seq data from Roadmap epigenomics…

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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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Merging genotyping array VCFs and then running kinship analysis

Merging genotyping array VCFs and then running kinship analysis 0 Hello, I have about 4200 array genotyping VCFs (from the Illumina Infinium CoreExome-24 Kit) and I have merged them using bcftools merge. The chip has 500K exonic SNPs. These are trio data – which means 1700 of them are probands,…

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One-hot encoding for PLINK or VCF

One-hot encoding for PLINK or VCF 0 I want to write an autoencoder for SNP data. Is there an established way to one-hot-encode binary PLINK or VCF input? I believe that can be done by manipulating PLINK’s bed file but am afraid to do something wrong. By one-hot encoding I…

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find positions of a short sequence in a genome

Here’s a demo Python script you can modify for your use, which suggests the rough principle: #!/usr/bin/env python import sys import re bed = “””chr1t0t10tABCDEFGHIJ chr1t5t15tFGHIJABCDO chr1t10t20tABCDOPABCD””” string_to_match = sys.argv[1] pattern = re.compile(string_to_match) for line in bed.split(“n”): (chr, start, stop, id) = line.split(“t”) for match in pattern.finditer(id): sys.stdout.write(“t”.join([chr, str(int(start) +…

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Interpretting phastConsElements from USCS Table Browser

Interpretting phastConsElements from USCS Table Browser 0 I am trying to understand the information present in PhastCons elements bed files from USCS Table Browser. Following the information I found here I managed to get a description of the column names, but not a description of what they are measuring. I…

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Plink –merge-list only outputting fam

Plink –merge-list only outputting fam 0 I am attempting to merge Plink files towards an algorithm I am using (CookHLA). I have already made the bed/bim/fam files for my vcf files. Now, I want to merge them into a single file so I can progress with the algorithm. To do…

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Count 5’End Mapped To A Specific Genomic Position

Count 5’End Mapped To A Specific Genomic Position 7 I got several SAM/BAM files, and I am interested in 5’ends of the mapped reads. Is there any tools or scripts to count how many 5’ends are mapped at a specific genomic position? N.B. I am not try to count the…

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P-values far too high for quantitative regenie phenotype

P-values far too high for quantitative regenie phenotype 0 Hi all, I’m having some trouble running regenie (v2.2.4) on a quantitative phenotype for a large cohort. I’m testing a standard height GWAS with heights rounded to the nearest integer. I’ve tried a few different tests to see where the issue…

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How to extract genomic upstream region of a protein identified by its NCBI accession number?

How to extract genomic upstream region of a protein identified by its NCBI accession number? 1 I have a list of NCBI protein accession numbers. I would like to extract out the upstream genomic region of the corresponding gene’s nucleotide sequence. I will be thankful to you if you can…

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Changing the sample IDs of a bed/bim/fam PLINK fileset

Changing the sample IDs of a bed/bim/fam PLINK fileset 0 Hi everyone, I am working with a genotype set that is not identified with the samples IDs that I want. However, I do have a lookup table which I can use in R to get the right identification when I…

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Aro Biotherapeutics hiring Investigator, Genetics & Bioinformatics in Philadelphia, Pennsylvania, United States

About Aro BioTx Join the team at Aro Biotherapeutics creating breakthrough biotherapeutics based on Centyrin oligonucleotide conjugates. Centyrins are small protein domains based on the fibronectin domains of human Tenascin C that combine the affinity and specificity properties of antibodies with the stability and tissue penetration properties of small molecules….

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bedtools getfasta concatenating sequences

bedtools getfasta concatenating sequences 0 Hi, I have a bed file containing exons of the genes. the name field is specified with name of the gene like (ENSG***). when I run bedtools getfasta I get the sequences of each exon separately. is there a standard way in order to concatenate…

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Bedtools: Merging Many Bed Files

Bedtools: Merging Many Bed Files 2 I am using the algorithm CookHLA for my research. As part of its preparation, I need to feed it a bed file representing at least 100 of my samples. I have made the bed files for 500 samples using samtools and bedtools in a…

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Create combined CpG and non-CpG bedgraphs for DNA methylation using Bismark

Create combined CpG and non-CpG bedgraphs for DNA methylation using Bismark 0 Hello, previously, I was using Bismark with the ‘–comprehensive’ option to generate the individual bedgraph files from which we made the bigWigs. For one particular figure, my boss wants me to generate merged bdg files so that we…

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How to transform a whole-genome callset into whole-exome callset?

How to transform a whole-genome callset into whole-exome callset? 0 Hi all, I have a callset from whole-genome data and with this callset, I want to transform it into exome callset by extracting the variants using a exome target interval. I obtained two exome target list, one from 1KG project…

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Submit sequence data to NCBI

Data provision and standards. GEO sequence submission procedures are designed to encourage provision of MINSEQE elements: Thorough descriptions of the biological samples under investigation, and procedures to which they were subjected. Thorough descriptions of the protocols used to generate and process the data. Request updates to accessioned records per the…

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How to pipe awk of bed file into samtools to extract fasta sequences?

How to pipe awk of bed file into samtools to extract fasta sequences? 1 I have a bed file (seq.bed) that contains “queryID queryStart queryEnd”. Following is the example (the content of seq.bed file). SRR5892231.6 28 178 SRR5892231.7 4 307 SRR5892231.7 16 307 SRR5892231.9 216 408 I would like to…

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How can I find reads for specific elements in a bam file?

Hi, I have a specific set of 1,009 elements in a bed file that I am interested in. I also have bam files which I would like to process to know the number of reads for these specific elements (for comparison purposes). I understand some simple uses of samtools commands,…

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Haplotype divergence supports long-term asexuality in the oribatid mite Oppiella nova

Significance Putatively ancient asexual species pose a challenge to theory because they appear to escape the predicted negative long-term consequences of asexuality. Although long-term asexuality is difficult to demonstrate, specific signatures of haplotype divergence, called the “Meselson effect,” are regarded as strong support for long-term asexuality. Here, we provide evidence…

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Question about ROH analysis by Plink 1.9

Hi all, I have recently tried to estimate runs of homozygosity (ROH) from my vcf file by using plink 1.9. I ran following code to generate binary files that plink required: plink –vcf myfile.vcf –make-bed –out out_name –no-sex –no-parents –no-fid –no-pheno –allow-extra-chr This vcf file only contains one individual and…

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Database for Enhancers with Coordinates

Database for Enhancers with Coordinates 4 Can anyone recommend some good databases for extracting bed files with enhancer coordinates. I have used UCSC in the past, I was hoping to find some alternatives ChIP-Seq genome • 163 views • link updated 11 minutes ago by Papyrus &starf; 1.3k • written…

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Visulization of raw 4C-seq reads in UCSC

Visulization of raw 4C-seq reads in UCSC 1 I’m trying to create bedGraph files to view raw and normalised reads from a 4C-seq experiment to view in UCSC for two biological replicates. Is there a simple way to do this? I’ve tried using bamCoverage and expected to get peaks for…

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How to download BED file with all the fields?

How to download BED file with all the fields? 2 Hello, my goal : to download a certain BED file from ucsc website that contains all these fields: bin chrom chromStart chromEnd name score strand signalValue pValue qValue peak I will describe my actions and my problem: – I go…

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how to to download a BED file from ucsc to directory using linux

how to to download a BED file from ucsc to directory using linux 2 Hello, my goal : to download a BED file as desribed here to my directory using linux commands . in the meantine, I am trying to download the wanted file directly in the following way: my…

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Why may BOLT-LMM and SAIGE (quantitative, linear-mixed model) yield different results when ran on the absolutely the same dataset?

As a validation experiment, I have run the same GWAS of a quantitative phenotype derived from the UKBiobank, alongside the genomic data from the UKBiobank, once using the program BOLT-LMM and once using SAIGE linear mixed model (with selected quantitative trait tag). I wanted to see if the results would…

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Agilent Sure Select .bed file v6 and v8

Agilent Sure Select .bed file v6 and v8 0 Hi, I would like to differentiate between the Agilent SureSelect .bed file version v6 & v8. The release notes is unclear and couldn’t arrive at any inference. I would like to differentiate and get the genomic regions and gene names as…

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Dnaman software manual

Dnaman software manual DNADynamo DNA Sequence Analysis SoftwareCLC Genomics Workbench – Qiagen They have sent a man to locate the key. He was making notes with a slim gold pen on a Gucci pad? When I married my husband, that all…

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How to get the nucleotide sequence through ORF information?

How to get the nucleotide sequence through ORF information? 0 I have a file with ORF information, including the start position and end position on the chromosome. At first I wanted to create a bed file, and then use the getFastaFromBed of bedtools to get the sequence. But I found…

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Exon coordinates and sequence

I did it like that: 1- Download refGene.txt.gz and hg19.fasta from the UCSC goldenpath. ( note: convert hg19.2bit to hg19.fa using twoBitToFa ) 2- Create a bed file with exon coordiniate using my awk script // to_transcript.awk BEGIN { OFS =”t” } { name=$2 name2=$13 sens = $4 ==”+” ?…

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SNP exon region UCSC

SNP exon region UCSC 2 how i can get SNP in only exons regions genome with UCSC? UCSC get the all SNP of gene region, and there is no filter option to get only exon region. tx ucsc SNP exon • 245 views • link updated 2 hours ago by…

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Phenotype file for eQTL analysis using GEMMA

Phenotype file for eQTL analysis using GEMMA 0 Hello All, I appreciate it if someone could direct me in this regard. I am running eQTL analysis using GEMMA software. I have corrected the expression file with all samples (280 samples) and the genotype file is (170). I have a couple…

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