Tag: bigWig

Inferring and perturbing cell fate regulomes in human brain organoids

Experimental methods Stem cell and organoid culture We used six human iPS cell lines (Hoik1, Wibj2, Kucg2 from the HipSci resource47; 409B2 from the RIKEN BRC cell bank; 01F49i-N-B7 (B7) from Institute of Molecular and Clinical Ophthalmology Basel; and WTC from the Allen Institute) and three human ES cell lines (H1-PAX6YFP…

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Bedtools Bam To Bed With Code Examples

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

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

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

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how to deal with these???

‘Negative’ and ‘Positive’ bigWig RNAseq files: how to deal with these??? 0 @bas_work-22458 Last seen 1 day ago Netherlands Hi: Before diving into analysis of (public) RNAseq data, I discovered that the data are stored in two BigWig files per sample (i.e. carrying a ‘neg’ identifier, the other a ‘pos’…

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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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Deeptools: computeMatrix can’t read file

Deeptools: computeMatrix can’t read file 1 Hi, I generated bigwig file using bamCoverage with the following code. bamCoverage -b A.bam -o A.bw –binSize 10 -p max –normalizeUsing CPM Then, I tried to use computeMatrix computeMatrix -S A.bw -R B.bw -o C but I got the following error usage: computeMatrix [-h]…

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What is the relationship between the value of the bigwig file generated by MACS2 and the read count?

What is the relationship between the value of the bigwig file generated by MACS2 and the read count? 0 What is the relationship between the value of the bigwig file generated by MACS2 and the read count? When using Deseq2 or edgeR to identify the differential peak, because the value…

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Gene Expression Prediction from DNA sequences

Gene Expression Prediction from DNA sequences 1 Hi everyone! I am a university student working on my Master’s thesis. I worked on a paper called Xpresso which has the purpose to predict the gene expression levels starting from DNA sequences using deep learning techniques. Now, my lecturers have asked me…

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How to identify differential enhancers?

How to identify differential enhancers? 0 Deseq2 or edgeR only allow the input of reads count to identify differential regions, but I get less differential enhancer with reads count, can I use the signal from the bigwig file as input to deseq2 or edgeR to identify the differential enhancer? EdgeR…

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Log2 Scale Deeptools

Greetings, I hope everyone is doing well. So I used computeMatrix from deeptools to calculate the coverage of certain samples. The bigwig signal is in BPM (generated by bamCoverage). I want to transform the values in the matrix to a log2 scale to get the enrichment profile or heatmap in…

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using rtracklayer to import bigwig files from http works with MacOS but not with Windows

We are using the package ‘rtracklayer’ to load and manipulate bigwig files as part of a larger script. We need to access bigwig files from an http-server, and we can do this smoothly on MacOS, but we can’t get it to work on Windows machines – while local bigwig files…

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MultiBigwigSummary of deepTools keeps on running for a long time

MultiBigwigSummary of deepTools keeps on running for a long time 1 I am trying to generate a merged bigwig file using multiBigwigSummary for using in the plotCorrelation tool in deepTools. However, the 8 files are running in this program for almost 5hours. How long does it usually take to generate…

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Multiple stages of evolutionary change in anthrax toxin receptor expression in humans

Human research participants We have complied with all relevant ethical regulations and informed consent was obtained from all participants. This work was approved by the Cornell University IRB under protocol 1506005662. Animal research This work was approved by the Cornell University IACUC under protocol 2009-0044. Welfare and handling of all…

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

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

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ChIP-seq heatmap input bed file

ChIP-seq heatmap input bed file 0 Hello, I am getting confused about the ChIP-seq heatmap concept. In particular, what should be the .bed file exactly? For example while using deeptools before plotHeatmap, computeMatrix is used and you should provide bigwig file and a bed file. Bigwig file should be the…

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Bioconductor – Bioconductor 3.14 Released

Home Bioconductor 3.14 Released October 27, 2021 Bioconductors: We are pleased to announce Bioconductor 3.14, consisting of 2083 software packages, 408 experiment data packages, 904 annotation packages, 29 workflows and 8 books. There are 89 new software packages, 13 new data experiment packages, 10 new annotation packages, 1 new workflow,…

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DESeq2 normalization when using with derfinder

Hi, I have a question about whether I should set the sizeFactors to 1 prior to using DESeq2 on the counts obtained from derfinder. I have normalized bigwig files ( using deepTools ), which I use as input to derfinder. Following the instructions in the users guide : lcolladotor.github.io/derfinder/articles/derfinder-users-guide.html#expressed-regions-level-1 My…

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Measure genome-wide agreement of peaks in

Measure genome-wide agreement of peaks in 0 Is there an approach to measure agreement in epigenomic signals e.g. histone marks (continuous -log10 p-vals after peak calling)? This approach should also work across assays or cell types. For example, how similar is the DNAse-seq signal across Neutrophils, Monocytes and T-cells? Are…

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What is bigwig file?

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

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

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

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ATAC-seq sample normalization

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

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

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

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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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difference between treat_pileup and bdgcmp fold enrichment tracks macs2

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

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How to get Read Counts from MACS2 output files?

How to get Read Counts from MACS2 output files? 0 Hello, I am working with GEO datasets that supply both bigwig(bw) and bed files for each ATAC sample. I need the read counts/pile up value for downstream analysis, but the 6+4 narrow peak file format from MACS2 does not include…

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Where can I get ?or how can I make a mappability track for hg38 assembly

Where can I get ?or how can I make a mappability track for hg38 assembly 2 Lucky you @manojmumar_bhosale I worked on similar problem recently and therefore have the bash script you can use. Required tools: GEM libary from here UCSC’s wigToBigWig from here (I chose binary for Linux 64…

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convert genomic bigWig file to transcriptome space

convert genomic bigWig file to transcriptome space 0 Hi all, Is anyone aware of a function to convert a bw file mapped to a genome to map to a transcriptome (of said genome), where the input would be the genomic bw file and gff/gtf/bed annotation and output a single ‘transcriptomic’…

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Get chromosome names of a bigwig file

Get chromosome names of a bigwig file 1 I would like to extract the chromosome names from a bigwig (.bw) file. Is there an existing tool/command? (I need to verify they match the genome annotation file I am working with + diagnose failing multiBigwigSummary) bigwig • 37 views • link…

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Download bigWig files of publicly available ChIP-seq samples

Download bigWig files of publicly available ChIP-seq samples 1 There are a couple of efforts to provide quality controls of publicly available ChIP-seq data sets (e.g. www.ngs-qc.org/ and CISTROME. But is there a way to obtain the normalized bigWig files? Cistrome, for example, allows you to explore the coverage data…

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

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

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STAR split reads into two strands

STAR split reads into two strands 0 Hi all, I’m trying to find a way to split reads mapped with STAR into two separate bam-files, one for each strand. STAR is able to do that when creating bedgraph or bigwig outputs (–outWigType and –outWigStrand), however I can not find any…

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CUTEVERYDAY.COM – Bedgraph to bigwig generates error

bedGraph chrom.sizes myBigWig.bw (Note that the bedGraphToBigWig program DOES NOT accept a gzipped bedGraph input file.) Move the newly … Source link

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Slavicx.com – Convert BAM to bigwig (parallel) · GitHub

Convert Sam To Bigwig Convert BAM into bigwig for chicken Hi, I used functions of “Create a BedGraph of genome coverage” and “Wig/BedGraph-to- … Source link

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bedGraphToBigWig Tutorial and Report

It is too easy to make error report in the bedGraphToBigWig process. I want to save the time for the fresh people. The following procedure would be work well for majority situations.  1, bedGraph should be without header before sorting awk ‘NR!=1’ input.bedGraph > input.deheader.bedGraph 2, bedGraph should be sorted sort…

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