Questions tagged [bed]

Browser Extensible Data, a collection of related plain text formats for describing genome features for visualization with genome browsers.

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1 answer
33 views

Chromosome position -> ENSP

I'd like a tabix file that, for every position in the genome, gives me a list of every ENSP within 5kb of that position. This should be easy right... I know VEP /kinda/ gives me this, but I'd rather ...
1 vote
1 answer
54 views

How to calculate distance between two regions from bed like dataframe in R?

I'm wondering how can I calculate the distance between two regions from the bed (chr, start, ...
0 votes
1 answer
82 views

Fastest way to convert GTF or GFF file to a BED file?

Given a GTF/GFF3 annotation file, what is the fastest way to convert it into a BED file?
1 vote
0 answers
45 views

tabix to subset each VCF by the coordinates given

I have a vcf file like below ...
1 vote
2 answers
68 views

How to visualize FIMO outputs?

I used FIMO to scan several of my promoter sequences for TF binding motifs. The output .tsv file gives me the motif name/sequence plus the start and stop location, how can I visualize these outputs to ...
2 votes
1 answer
109 views

CNVKit does not output all the accessible regions in the targets bed file

This question was also asked on Biostars I am using CNVkit on my data using hg38 as reference. The command that I am using is the following: ...
3 votes
1 answer
145 views

How can I convert a BED file to GTF/GFF with gene_ids?

Given a .bed (BED12), how can I convert it to GTF/GFF formats with gene_id attributes? What is the fastest way or available tools to do it? For example, given an input like this: ...
17 votes
7 answers
6k views

How to convert BED to GFF3

I would like to convert a BED format to GFF3. The only useful tool that I could find via a google search seems to be Galaxy, ...
2 votes
2 answers
3k views

bigWig to bed for regions above/below threshold

I'd like to threshold a bigWig file on a value and get all regions above or below that value in bed format. Ideally without too many file conversions. Are there any tools to do that?
3 votes
1 answer
115 views

Why doesn't bedtools getfasta pick up the first base?

I am using bedtools getfasta to convert genomic coordinates to sequences. I feed it a bedfile containing say chr1 s.start s.end. When I check the sequence output, it does not include the s.start base. ...
1 vote
1 answer
98 views

obtaining a fragment data file bed from bam

Im trying to follow this pipeline https://github.com/epifluidlab/cragr on cfDNA WGS. I have bam files from paired end reads aligned with bwa mem. The workflow requires bgzipped and indexed fragment ...
0 votes
1 answer
49 views

How can I change all text in a .tsv file to 1, except the first three fields?

I want to convert a .tsv file table in binary format (1 and 0). In which all cells containing text would become 1 and blank cells would become ...
1 vote
3 answers
249 views

How to join multiple large .tsv (> 20 GB, bed file) files by two identifier?

This question has also been asked on Biostars I wonder how can I join multiple large .tsv files (over 20 GB each) by using two identifiers (columns) which I used to do using the ...
3 votes
2 answers
78 views

Create bed file where each column is the number of intersections with another bed file

For example I have 3 bed files: window.bed: chr1 0 1000 chr1 1000 2000 lp1.bed: ...
1 vote
1 answer
114 views

How to get a file with the introns of a gene?

I was able to get the exons of a particular gene as a fasta file from the NCBI genome viewer. As for introns I only found a bed file that showed where the intron starts and ends, along with its ...
6 votes
3 answers
2k views

How can I compare two bed files?

I am trying to translate (lift over) bed files describing genomic regions from hg37 to hg38. I have tried both UCSC's LiftOver tool and CrossMap but saw that they give me different results. I ...
0 votes
1 answer
55 views

Problem with ClinCNV script

I have some problems with ClinCNV: My input: ...
0 votes
2 answers
2k views

plink: --update-name vs. editing the BIM

I am working with data from the HGDP public files. These are massive VCFs from whole genome sequencing. To begin with, I converted these to BEDs using plink (1.9). The next problem is that these files ...
1 vote
1 answer
57 views

Problems with BED format for ClinCNV

I have some problems with ClinCNV(https://github.com/imgag/ClinCNV): I made a BED file from a BAM, then i made a GC count with ngs-bits (link: https://github.com/imgag/ngs-bits ) The main idea of ...
1 vote
1 answer
825 views

Need to convert .bed to .vcf. Can the reference build (and necessary .fasta) be determined for a .bed file?

I have some .bed files (and .bim and .fam files) containing data for a number of different samples, and I need to convert them to .vcf. I've found bed2vcf which is ...
9 votes
2 answers
726 views

How to import a large amount of .bed, .gff, .vcf, .paf, .sam files into an SQL database?

Are there best practices to load different bioinformatics file formats such as VCF, BED, GFF, and SAM to SQL databases? I am wondering how people out there do that efficiently. All of these three ...
5 votes
2 answers
3k views

How can I easily get the read size distribution of reads mapping on a certain set of regions?

Suppose I have a BAM file indicating where reads in a library have mapped, and a bed file describing a set of genomic regions. Is there a way to easily get the size distribution of the reads mapping ...
2 votes
1 answer
154 views

Count reads at specific gene features

I have BAM files from an RNA-Seq experiment and for all genes (or a subset) I want to get the number of reads in regions around the TSS (e.g. 2kbp) and the TES (e.g. 2 kbp) and calculate the ratio ...
2 votes
1 answer
194 views

gtf2bed only retains gene information

I want to convert an hg38 GTF file to bed format using gtf2bed: ...
1 vote
0 answers
155 views

chip seq biological replicate merge after peak-calling

I have 3 biological replicates for KO condition. What I have done so far Peak calling The removed blacklisted region Now Im bit confused about the peak merging stage. Here Im trying to use the ...
4 votes
1 answer
856 views

Making a bed file for RSeQC

I making a bed file for RSeQC, so it can do things like compute the number of reads from exons, introns, 5"UTRs, etc. I want to use a bed file that corresponds to my GTF file, so I use gtf2bed to ...
1 vote
2 answers
1k views

Extract only exon regions from GFF/GTF file with input bed regions

I have a bed file that contains a list of regions and I would like to extract only the exon regions from a GTF/GFF file that are contained in the given regions. Is there a simple command or tool that ...
2 votes
1 answer
102 views

Where to get BED files for regions that contain binding site motifs for specific transcription factors?

Quick question, is there a place where one can download BED files for the binding motifs of certain transcription factors. In my case, I'm looking for a BED file for the genomic regions (enhancers) ...
1 vote
1 answer
674 views

Plink error: --check-sex/--impute-sex requires at least one polymorphic X chromosome locus

I am running an analysis in plink. This is my first attempt at a QC and I keep encountering the same message when I try to go through with my sex check. I've done the SNP missingness step, it's this ...
14 votes
3 answers
14k views

How to obtain .bed file with coordinates of all genes

I want to get a .bed file with the genes' names and canonical coordinates, also I would like to have coordinates of exons, too. I can get the list from UCSC, however, if I choose UCSC Genes - ...
9 votes
2 answers
2k views

5'UTR and 3'UTR annotation in yeast

I am working on a project in which I need to compute several parameters (such GC content and length) of 5'UTR and 3'UTR sequences of Saccharomyces cerevisiae yeast genes. The problem is finding a ...
3 votes
1 answer
109 views

Defining a bedfile for chromosome X without pseudo-autosomal regions

I would like to define a bedfile for chromosome X, to target only basepairs outside of pseudo-autosomal regions (and going forward other regions, too). First, I wasn't able to find an already prepared ...
1 vote
2 answers
2k views

Create BED file from list with gene symbols

Is there a way to generate a BED file of a list of gene symbols for a given genome?
3 votes
5 answers
7k views

How to create a .bed file from .fasta? [duplicate]

I have some problems in creating a .bed file for hg19, so I will be able to visualize the .bed file in IGV. The .fasta file contains rows of this form: ...
8 votes
5 answers
3k views

Merging bed records based on name

I generated a file starting with the following bed lines: ...
2 votes
1 answer
1k views

How to split bedfile into non-overlapping regions and compute aggregation function on duplicate segments

I have a bed-like file in which I have several overlapping regions with associated features. I want to split the overlapping regions into disjoint regions in order to process the file (e.g. with ...
0 votes
1 answer
90 views

How can I add for several bed files the header : track type=narrowPeak name=“narrowPeak” preferably in python ,can handle with R

I want to create custom tracks from these files I can add the line : track type=narrowPeak name=“narrowPeak” manually by opening it with text editor: track type=narrowPeak name=“narrowPeak” but I ...
0 votes
1 answer
418 views

How to visualize called narrowPeak files in UCSC Genome browser? [closed]

I have this file: and I get this error I googled and found this solution but it still doesn't work and I get this error Error File 'GSM2797523_FOXA2_IDR0.02_narrowPeak_try.bed' - line 1 of custom ...
1 vote
1 answer
555 views

Time for running ADMIXTURE analysis

I am trying to run the ADMIXTURE software for the first time to analyse the structure of an in-house dataset of samples comparing to 1000 genomes project ancestral populations. I am trying to ...
2 votes
3 answers
1k views

Get start and end coordinates per chromosome

I will use GATK for SNP calling (HaplotypeCaller). I need to feed the interval file in the command, otherwise I get errors (even though I want to use the whole genome, not a subset - btw it's not the ...
1 vote
0 answers
41 views

How to get the splicing regions (BED) of all genes for Human GRCh38?

How can I obtain a BED file that describes the splicing sites of all genes for GRCh38 human genome ? Thank you
6 votes
1 answer
495 views

How to filter out cross alignments from a BED file?

I have a BAM file: ...
2 votes
2 answers
588 views

Efficiently iterate over bed and subset pyranges objects

I am using pyranges and I have two datasets that I want to compare in several genome-wide intervals based on a bed file. For every interval in the bed file, I want to get all overlapping positions ...
7 votes
6 answers
2k views

bed file with N regions of GRCh38 reference?

How do I obtain a bed file with the list of N-regions of GRCh38 reference? This is, the regions where the sequence is a stretch of Ns.
5 votes
4 answers
2k views

Range overlap python error with genomic regions

I have two files s3.txt : 1 10 20 1 5 20 2 20 30 2 25 30 1 10 50 2 20 60 1 14 17 s4.txt: 1 10 20 2 20 30 I am trying to match col0 ...
2 votes
1 answer
436 views

BED file from .bam alignment structure

I am using a pipeline from nanopore to detect structural variants (SVs) in a human sample with long-reads sequencing. The first steps of the pipeline are: index the reference genome with ...
2 votes
1 answer
103 views

UCSC liftover cannot produce bed format output

I was trying to use UCSC liftover tool to convert human coordinates to mouse. While most of the files worked, one file didn't: ...
6 votes
4 answers
996 views

Any fast options to query large VCF bed intervals?

I'm doing some analysis and I need to subset a large VCF file (~8GB gziped) given a bed interval and identify within a subset of rsid. Unfortunately, both my normal choices to do this analysis (<...
7 votes
2 answers
135 views

How to release an R package with several bed files?

I'm currently creating an R package, and my scripts require before any analysis is done that 1-2 bed files be loaded. Normally, I would run the scripts with the following: ...
1 vote
0 answers
331 views

bedtools single-nucleotide coverage in BED-specified regions for multiple BAMs

I have a BED6 (BED + name, score, strand info) file that defines some regions of interest. I also have a set of BAMs corresponding to different samples. I would like to obtain output similar to <...