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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8
votes
3answers
209 views

How to import large .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 ...
8
votes
2answers
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
1answer
44 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
votes
2answers
79 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
5answers
4k 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: ...
7
votes
5answers
2k views

Merging bed records based on name

I generated a file starting with the following bed lines: ...
2
votes
1answer
860 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
1answer
31 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
1answer
71 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 ...
0
votes
2answers
657 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
1answer
176 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
3answers
395 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 ...
6
votes
3answers
1k 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 ...
1
vote
0answers
33 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
2
votes
2answers
355 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
6answers
1k 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
4answers
1k 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 ...
1
vote
1answer
183 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
1answer
56 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: ...
2
votes
0answers
461 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 ...
6
votes
4answers
506 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
2answers
116 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
0answers
241 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 <...
6
votes
3answers
316 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 ...
13
votes
3answers
10k 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 - ...
6
votes
1answer
134 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 ...
3
votes
1answer
50 views

How to apply function on bedfile based on a reference bedfile

I have two bed-like files: File1 ...
2
votes
1answer
403 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: ...
5
votes
2answers
1k 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 ...
3
votes
2answers
171 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 ...
1
vote
3answers
2k 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 ...
0
votes
2answers
324 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 ...
2
votes
2answers
401 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 ...
1
vote
1answer
122 views

TruSeq Exome Kit bed file old version

I have to run an analysis using Whole Exome Sequencing (WXS) data prepared with the TruSeq Exome Kit (2012). I need the .bed file for the kit and I found it here. ...
2
votes
2answers
2k 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
1answer
514 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 ...
13
votes
4answers
4k 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, ...
18
votes
3answers
3k 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 ...
4
votes
2answers
219 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: ...
9
votes
4answers
217 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 ...
19
votes
7answers
9k views

How to convert FASTA to BED

I have a FASTA file: ...
6
votes
1answer
68 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 ...