Skip to main content

Questions tagged [bed]

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

Filter by
Sorted by
Tagged with
18 votes
7 answers
17k views

How to convert FASTA to BED

I have a FASTA file: ...
SmallChess's user avatar
  • 2,709
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, ...
aechchiki's user avatar
  • 2,676
17 votes
3 answers
5k views

Convert a BAM file from one reference to another?

I have a set of BAM files that are aligned using the NCBI GRCh37 human genome reference (with the chromosome names as NC_000001.10) but I want to analyze it using a BED file that has the UCSC hg19 ...
morgantaschuk's user avatar
15 votes
3 answers
15k 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 - ...
German Demidov's user avatar
10 votes
4 answers
283 views

Annotation format design

Bashing file formats is a favorite pastime in bioinformatics, and annotation file formats such as GFF and BED seem to get special attention. A lot of this frustration stems from community's shockingly ...
Daniel Standage'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
  • 1,042
9 votes
2 answers
789 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
  • 1,437
8 votes
5 answers
3k views

Merging bed records based on name

I generated a file starting with the following bed lines: ...
bli's user avatar
  • 3,130
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
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: ...
ShanZhengYang's user avatar
6 votes
3 answers
448 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
  • 1,813
6 votes
4 answers
1k 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 (<...
andremrsantos's user avatar
6 votes
1 answer
496 views

How to filter out cross alignments from a BED file?

I have a BAM file: ...
SmallChess's user avatar
  • 2,709
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 ...
terdon's user avatar
  • 10.2k
6 votes
1 answer
110 views

What's the scaling for HOMER metagenes?

I'm trying to use HOMER to make a metagene profile over gene bodies using a bedgraph file I've generated. The problem is that every time I do, I get really weird scaling on the y-axis. I should be ...
bioinform_noob's user avatar
6 votes
1 answer
221 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
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 ...
novicebioinforesearcher's user avatar
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
273 views

After artificially creating events in a FASTA file, how do I keep track of the old coordinates?

I'm beginning with the reference genome in FASTA format, hg19. I am reading the sequence into a Python dictionary with BioPython: ...
ShanZhengYang's user avatar
4 votes
1 answer
933 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
  • 573
4 votes
2 answers
323 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
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
  • 1,437
3 votes
1 answer
346 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
2 answers
85 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: ...
rscott's user avatar
  • 31
3 votes
1 answer
96 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, ...
Deb's user avatar
  • 289
3 votes
1 answer
143 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
3 votes
1 answer
113 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
  • 1,813
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
  • 1,813
3 votes
1 answer
817 views

Dealing with indels when converting a position to chromStart and chromEnd for a bed file

Starting with a chromosome # and position, I am trying to get chromStart and chromEnd values for a .bed file, but I am not sure how to calculate chromEnd when I have a variant that is an insertion or ...
Sarah's user avatar
  • 516
3 votes
1 answer
24 views

How to convert bed to wig file!

I was wondering how can I convert bed file to wig file. I have several bed files which look like ...
Deb's user avatar
  • 289
2 votes
2 answers
744 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
  • 1,804
2 votes
1 answer
567 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
2 votes
1 answer
467 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
164 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
222 views

gtf2bed only retains gene information

I want to convert an hg38 GTF file to bed format using gtf2bed: ...
justinian482's user avatar
2 votes
2 answers
627 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
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
  • 1,813
2 votes
3 answers
2k 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
  • 2,676
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
2 votes
1 answer
113 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
2 votes
1 answer
107 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
  • 292
2 votes
1 answer
128 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
1 vote
2 answers
2k 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
  • 195
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
1 vote
3 answers
259 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
  • 289
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
  • 14.3k
1 vote
1 answer
37 views

R: How to measure mean of a column for every 10000 rows condition on other column?

I have a large bed-like dataframe with over 30 million rows. What is the best way to calculate the mean value of fourth column ...
Deb's user avatar
  • 289
1 vote
1 answer
164 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
  • 21
1 vote
1 answer
1k 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
1 vote
1 answer
624 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