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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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, ...
Deb's user avatar
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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?
Alejandro Gonzales-Irribarren's user avatar
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tabix to subset each VCF by the coordinates given

I have a vcf file like below ...
Zizogolu's user avatar
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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 ...
Dan Bolser's user avatar
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 ...
JohnDoe23's user avatar
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: ...
Alejandro Gonzales-Irribarren's user avatar
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. ...
venkatesh war's user avatar
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 ...
Julieta's user avatar
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1 answer
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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 ...
Deb's user avatar
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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 ...
Deb's user avatar
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3 votes
2 answers
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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: ...
rscott's user avatar
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1 answer
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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 ...
venkatesh war's user avatar
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1 answer
55 views

Problem with ClinCNV script

I have some problems with ClinCNV: My input: ...
Илья Бетяев's user avatar
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 ...
Илья Бетяев's user avatar
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 ...
Jackson Xavier's user avatar
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: ...
ashenflower's user avatar
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 ...
justinian482's user avatar
2 votes
1 answer
194 views

gtf2bed only retains gene information

I want to convert an hg38 GTF file to bed format using gtf2bed: ...
justinian482's user avatar
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 ...
kcm's user avatar
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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 ...
SBDK8219's user avatar
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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) ...
user305902's user avatar
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 ...
pvp's user avatar
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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 ...
gc5's user avatar
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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?
justinian482's user avatar
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 ...
0x90's user avatar
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0 votes
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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 ...
Libby Kosolapov's user avatar
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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 ...
Libby Kosolapov's user avatar
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 ...
CoderGuy123's user avatar
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 ...
Iriel's user avatar
  • 31
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 ...
aechchiki's user avatar
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1 vote
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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
user324810's user avatar
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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 ...
Wouter De Coster's user avatar
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 ...
BCArg's user avatar
  • 283
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: ...
Code42's user avatar
  • 282
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 ...
Freek's user avatar
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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 <...
merv's user avatar
  • 651
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: ...
0x90's user avatar
  • 1,427
6 votes
3 answers
438 views

Fast filtering of intervals not falling within a certain distance from known genes

I would like to filter a bed file with intervals, ie. in the format of: chr1 13800 14301 chr1 15500 16001 chr1 19400 19901 chr1 22800 23301 ...
gc5's user avatar
  • 1,783
6 votes
1 answer
217 views

Generating random BED intervals given constraints

Problem is to generate a random BED interval given the following constraints: minimum start maximum end fixed length maximum ...
victorlin's user avatar
  • 161
3 votes
1 answer
58 views

How to apply function on bedfile based on a reference bedfile

I have two bed-like files: File1 ...
gc5's user avatar
  • 1,783
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 ...
gc5's user avatar
  • 1,783
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 ...
bli's user avatar
  • 3,130
4 votes
2 answers
315 views

Filter bam using SNP list in bed format with minimum mapping quality and base quality

I have a bam file and a bed file that defines a list of SNPs. I would like to filter the bam file to contain only those reads with a minimum mapping quality that overlap at least one SNP with a ...
mattm's user avatar
  • 754
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.
719016's user avatar
  • 2,324
2 votes
1 answer
551 views

bed file merge book-end features only if same name in column 4

I have a bed file where some entries have the same name in column 4 but are book-ended in coordinates, e.g. see below: ...
719016's user avatar
  • 2,324
1 vote
3 answers
4k views

Finding the nearest gene to a specified gene region

I've got some data on genomic regions of interest in a bedgraph-like format from the Mus musculus [mm10] genome, and would like to find out the nearest gene to these regions. Some of the regions will ...
gringer's user avatar
  • 13.9k
0 votes
2 answers
454 views

bed entries collapse based on score column

I have a bed file where some entries have the exact same chr:start-end but change in the name and score column. I would like to apply bedtools or a similar tool to obtain a filtered file where for ...
719016's user avatar
  • 2,324
2 votes
2 answers
725 views

Parse out exon coordinates from bed file for each gene

This is my bed file for all the exon coordinates I want to take out all the exons of a given gene. Let say I have gene in chr 1 which starts from chr1 11868 12227 ...
kcm's user avatar
  • 1,794
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?
isthisthat's user avatar
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 ...
plat's user avatar
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