Tag: BEDtools

How to merge samples of the same cell type to do differential peak calling? 1 Hi! Now I have 6 ATAC-seq samples which have been aligned to hg19 and called peaks by MACS2. 3 of them are from A cells and the other are from B cells. Now I’m going…

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How does “bedtools intersect -s” work with paired-end sequences? 1 Hi, I have paired-end lectures from RNAseq experiments and I want to use bedtools intersect with the force “strandedness” parameter (-s). Will bedtools take into account the paired-end reads and treat them as a single event, or will get two…

Merging Bed files with depth information 1 Hi, I was trying to merge a bed file which also has depth (I mean how many times was it seen on that bed file) information. I am only interested in one bed file not multiple files. For example my bed file is…

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R: Main bedtools wrapper function. tabix {bedr} R Documentation Main bedtools wrapper function. Description Main bedtools wrapper function. Usage tabix( region, file.name, params = NULL, tmpDir = NULL, deleteTmpDir = TRUE, outputDir = NULL, outputFile = NULL, check.zero.based = TRUE, check.chr = TRUE, check.valid = TRUE, check.sort = TRUE, check.merge…

Prerequisites Data An annotated genome Long reads Repeat annotation Software minimap2 samtools bedtools – for comparisons only tabix – for visualization only Installation 1 2 3 /work/gif/remkv6/USDA/04_TEJumper conda create -n svim_env –channel bioconda svim source activate svim_env Map your long reads to your genome with minimap My directory locale 1…

Bedtools genomecov – Bam to bedgraph conversion 1 Dear all, I would like to convert sorted and indexed bam file (~20GB) to an bedgraph file and used the following command: bedtools genomecov -bg -split -strand – -ibam sorted.bam It’s been 3 days since I executed the command, still I couldn’t…

Cnv Visualization 4 I’ve produced a list of CNV(copy number variation) data like below: chr10 10271614 10659796 DEL chr10 107242905 107243436 DEL chr10 107940570 107941687 DEL chr10 108020235 108022638 DEL chr10 111562017 111568300 DEL chr10 116956782 117389734 DEL chr10 117005207 117396827 DEL Just wondering if we have any VISUALIZATION software…

bcftools consensus -m file.bed error 0 Hi everyone, with bcftools consensus I’m trying to substitute the regions with low coverage with ‘N’. I made a BED file from the bam file with bedtools: bedtools genomecov -bga -ibam [file.bam] | awk ‘$4<5’ > low_coverage.bed output: 1 0 10001 0 1 10001…

merging .narrowPeak files with all of the columns they have 0 Hello, I want to ask about merging concept of .narrowPeak files generated by macs2. I am merging them with HOMER mergePeaks as I found the most informative one (compared to the bedops, bedtools). However, for the downstream analyses I…

genomecov VS bamCoverage 0 Hello, can someone help me understand the differences between bedtools’ genomecov and deepTools’ bamCoverage? Are they used interchangeably, are there key differences, can I generate the same results with both tools? I have sequencing data from a paired-end PRO-seq experiment and for generating the coverage tracks…

Significance Extrachromosomal circular DNA (eccDNA) plays a role in human diseases such as cancer, but little is known about the impact of eccDNA in healthy human biology. Since eccDNA is a tiny fraction of nuclear DNA, artificial amplification has been employed to increase eccDNA amounts, resulting in the loss of…

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…

bed intersect to get gene names from bed 0 Hi, I have a bed file for the baits and I want to get a list of targeted genes. So I downloaded a bed file from UCSC with the settings below and used bedtools to intersect. But I end up having…

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

bedtools annotate 0 Sorry for the trivial question but I can’t understand the numbers in the fraction of each feature in bedtools annotate. Example from website: $ cat variants.bed chr1 100 200 nasty 1 – chr2 500 1000 ugly 2 + chr3 1000 5000 big 3 – $ cat genes.bed…

sciClone input vaf file? 3 Dear All, Hi, I want to use sciclone on our exome sequencing data. but one thing I can’t understand that is how can I got varCount equal to 0? I have no idea about this, following data i just grep from sciclone-meta-master manuscript figure3 data…

understanding exercise on file coverage 0 I’m doing an exercise that asks for two files: Input 1: A target file (.bed format) contains multiple regions from chr7:40000000-50000000 of human reference genome GRCh37 (hg19) Input 2: Refseq exon list file (.bed format) for all human coding genes (hg19 position) The final…

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Memory Efficient Bedtools Sort And Merge With Millions Of Entries? 4 I would like to know if there is a memory-efficent way of sorting and merging a large amount of bed files, each of them containing millions of entries, into a single bed file that merges the entries, either duplicated…

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Error in gff file 1 I am trying to use gff with bedtools intersect to get the reads count to the gene. However, it is throwing an error: Error: Invalid record in file “obtectus_HiC.gff”. Record is HiC_scaffold_1502 maker gene -246 584 . + . ID “maker-@000032F|arrow|arrow-snap-gene-3.48”; Name “maker-@000032F|arrow|arrow-snap-gene-3.48”; Any idea…

bedtools getfasta does not give a proper fasta output 2 I have a problem with the output from bedtools getfasta, it used to work before. My bed-file looks like this – C1_64090263 131 164 C1_64090263-1:33 V1_87574936:0 – 33 0 And I am using the command –bedtools getfasta -fi in.fa -bed…

calculate nucleotides frequencies from mapped reads in a BAM file 0 Hi, Biostars forum members, I have a sorted BAM file generated from mRNA-seq experiments (aligned to human genome hg38). I would like to calculate the mono- and dinucleotides frequencies of the mapped reads in the BAM file (e.g. frequencies…

I’m trying to calculate the depth of coverage from my WXS data. Using Qualimap, I first used as the feature file the Gencode human genome (release 38) .gtf file associated with the genome I aligned to: feat=”gencode.v38.primary_assembly.annotation.gtf” for ea in *bam do $qualimap bamqc –java-mem-size=20G -bam $ea –feature-file $feat done;…

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Significance Proteins are the key drivers of neuronal synaptic function. The regulation of gene expression is important for the formation and modification of synapses throughout the lifespan. The complexity of dendrites and axons imposes unique challenges for protein supply at remote locations. The discovery of messenger RNAs (mRNAs) and ribosomes…

Counting the number of SNPs (VCF) for each genomic coordinates (BED) 1 I want to count the number of recorded variations for each genomic coordinates of a .bed file from the corresponding .vcf file. I guess it should be solved by vcftools, but I could not find any suitable option…

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…

bedtools.rb | searchcode PageRenderTime 19ms CodeModel.GetById 16ms app.highlight 1ms RepoModel.GetById 1ms app.codeStats 0ms /Library/Formula/bedtools.rb github.com/clouded-eas/homebrew Ruby |…

How to study transposable elements expression relationship with its closest gene? 0 Hello, I would like to post a question about an analysis that I need to do for my project. In my project we are studying the deregulation of transposable elements and genes with RNA-seq. We have obtained deregulated…

ps. sorry if my english is not too good, it is not my native language XD No te preocupes – tu inglés es excelente. —————— The main input that you require for GISTIC is the segmentation file, which should have: (1) Sample (sample name) (2) Chromosome (chromosome number) (3) Start…

bed2vcf (bedr) package error 0 Greetings, I am running bedr package in R to generate vcf file from bed file using reference as one of the arguments. I followed steps below: Sort bed file using bedtools intersect Convert sorted bed file to dataframe using read.table Change datatype for chr positions…

How to use MACS2 output for DESEQ2 differential analysis during ATAC-seq? How to get the intersect? 0 I have processed my ATAC-seq reads and finally obtained MACs2 output bed files. I am at a loss to proceed from here to DESeq2 analysis. I will be thankful to you if could…

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…

Create genome-unique intervals from overlapping records in a bed file 0 Let there exist a bed file, a, with 3 overlapping records: a chr1 1 20 s1 1 + chr1 5 20 s2 1 + chr1 10 20 s3 1 + I want to write a function which would parse…

Tools To Calculate Average Coverage For A Bam File? 12 I would like to get the average coverage of all the captured bases in a bam file. What would be the best way to do this? What I am looking is a simple one number like 40X. Given that there…

I used the following commands: bedtools shift -i ENCFF219OVU.bed -g mus_musculus.genome -s 0.5 -pct > peaks_centered.bed However, peaks_centered.bed was the exact same as ENCFF219OVU.bed. I went into the source code and identified the issue. The shift is stored in an integer value. Therefore, the float value 0.5 is lost. I…

I’d like to use bedtools to create strand-specific per-base coverage profiles for my paired-end bam alignments of stranded RNA-seq data. Existing Biostars answers here and here suggest using bedtools genomecov with the -5 option to extract only coverage from the 5′ ends of fragments. These are the commands that I’ve…

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…

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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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…

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…

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…

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…

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…

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 ==”+” ?…

Intersecting compressed gVCF with bed file 1 This may be a ridiculously simple question to ask but, I have a compressed genomic VCF file generated by the Strelka germline variant caller, with lines like the following, where no variation was detected: chr1 27394730 . T . . PASS END=27394756;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP…

Merge regions in bedgraph file 1 I have a bedgraph file with the chromosome, start and end point, and the coverage: CM000994.3 10167710 10167711 95 CM000994.3 10167718 10167720 95 I want to merge regions that are close together. With a bed file I could use something like this: bedtools merge…

# this should do it, concatenate peak locations in all peaks, sort them and merge cat A B C …. | sort -k1,1 -k2,2n | mergeBed -i stdin > locations.bed To know which files the peaks co-ordinates are merged from, you need to have an identifier in each file before…

Disclaimer: I may use coverage and ‘mean read depth’ interchangeably in this post. I’m refering to the average, per-base read depth. I’m running and compaing some mean coverage estimates for some specific bed regions on my bam files using bedtools; however, I’m having trouble finding the correct way to do…

Hello, I got a very weird output from BWA-mem2 – most of the reads have mapping quality of 0, even though there is no secondary alignment or anything else suspicious. I got sequencing data that was aligned with Novoalign to hg18, the data was bam files. I needed to realign…

read count to gene 0 I am using this command to get read counts to gene by using the bedtools intersect. samtools view -Shu -q10 -@ 20 UE-2955-CMLib12_sorted.bam | bedtools intersect -c -a GCA_900659725.1_ASM90065972v1_genomic.gff -b stdin > UE-2955-CMLib{i}_intersect_counts2.bed The command work for other files but not for one file. Which…

Normalization and differential analysis in ATAC-seq data 2 Hello everyone! I would like to know if someone had experiences with normalization and differential expression on ATAC-seq data. After using MACS2 for the peak calling, how can we use Dseq2 or EdgeR on these datas? Someone try this? What is the…

Fasta.fai file error 0 Hi, I have been struggling with an error in bedtools intersect. The command I am trying to run is as follows bedtools intersect -a sorted.vcf -b nstd166.GRCh38.variant_call_chr.vcf.gz -wo -sorted -f 0.8 -r -g Homo_sapiens_assembly38.fasta.fai For some of the files that I am assessing, I don’t get…

How To Uncompress The 1000 Genome Vcf.Gz File 2 Hello, Can somebody tell me how to uncompress 1000 Genome vcf.gz files? I am performing an RNA-editing analysis and would like to substract annotated SNPs/INDELs. I have already done so using dbSNP data with bedtools instersect, but am still stuck with…

Bedtools – converting multiple bam files to bed 1 Hi all, I have previous experience in R, but since some months ago I am trying new things in Python (JupyterLab). I have a a directory with different files. Some of them are ‘.bam’ files. My objective is to obtain ‘.bed’…

from keras.layers import Conv2D from keras.layers import AveragePooling2D from janggu import inputlayer from janggu import outputconv from janggu import DnaConv2D from janggu.data import ReduceDim # load the dataset which consists of # 1) a reference genome REFGENOME = resource_filename(‘janggu’, ‘resources/pseudo_genome.fa’) # 2) ROI contains regions spanning positive and negative examples…

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Thu, 02 Sep 2021 06:54:44 +0200 Source: bedtools Architecture: source Version: 2.30.0+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Andreas Tille <ti…@debian.org> Changes: bedtools (2.30.0+dfsg-2) unstable; urgency=medium . [ Steffen Möller ] * Update metadata – indent,…

If you wonder what an image and a container is, please see : Building an image starts from a Dockerfile which is a plain text file with instructions. Here an example which we are going to build: It is based on the mambaforge image, so mamba is already installed which…

Intersecting Encode peaks to search for tissue specific peaks? 0 As per the title, I have a list of H3K27ac peaks from my lab, and I would like to find out which of those are specific to my organ of interest. What I’ve decided to do was to download a…

It looks like you have a .gtf file. That means you can extract the exon lines from the .gtf file and count and sum up the exonic intervals. You can generate a sorted .bed file of exon coordinates by: grep -P ‘texont’ your.gtf | cut -f 1,4,5 | sort -k1,1…

Get chromosome sizes from fasta file 4 Hello, I’m wondering whether there is a program that could calculate chromosome sizes from any fasta file? The idea is to generate a tab file like the one expected in bedtools genomecov for example. I know there’s the fetchChromSize program from UCSC, but…

Pybedtools error sans 20-08-2021 pysam – Error when I install samtools for python on windows – i trying install pysam, pybedtools modules on python got error: ($i=1; $i[email protected] temp]$ conda install pysam bedtools hisat2 [ snip. However,…

Merge regions in bedtools genomecov/bedgraph file 0 I want to calculate the number of reads mapping to regions of the genome, and I want to group these reads into bins of say 1kb. I have used bedtools genomecov to generate a bedgraph file that shows the coverage of reads across…

extract entire header from BED file to FASTA 1 Hi, Is there any way one can extract the entire header from a BED file while using bedtools getfasta command and write it in the FASTA output ? Have tried using bedtools getfasta -fi hg19.fa -bed file.bed -fo test.fasta -fullHeader but…

How to convert mapping bam file to fastq without loseing the mapping information 0 Hi all, I want to create my RNA mapping data into a library for further analysis. Now I have bowtie2 mapping data, which is in bam files, I now use bedtools to extract fastq mapping reads…