Questions tagged [bed]
Browser Extensible Data, a collection of related plain text formats for describing genome features for visualization with genome browsers.
60
questions
3
votes
1
answer
33
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:
...
3
votes
1
answer
106
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.
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- 105
1
vote
1
answer
56
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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 ...
- 21
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 ...
- 65
1
vote
3
answers
244
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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 ...
- 65
3
votes
2
answers
76
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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:
...
- 31
1
vote
1
answer
95
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 ...
- 105
0
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1
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48
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1
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1
answer
53
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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 ...
- 15
1
vote
1
answer
695
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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 ...
2
votes
1
answer
99
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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:
...
- 21
2
votes
1
answer
147
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 ...
- 335
2
votes
1
answer
173
views
gtf2bed only retains gene information
I want to convert an hg38 GTF file to bed format using gtf2bed:
...
- 335
1
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0
answers
143
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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 ...
- 1,784
1
vote
2
answers
1k
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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 ...
- 195
2
votes
1
answer
95
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) ...
- 29
1
vote
1
answer
618
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 ...
- 67
3
votes
1
answer
102
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 ...
- 1,783
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?
- 335
9
votes
2
answers
649
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 ...
- 1,427
0
votes
1
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85
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
385
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
2
answers
2k
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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 ...
- 191
1
vote
1
answer
513
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 ...
- 31
2
votes
3
answers
1k
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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 ...
- 2,676
1
vote
0
answers
40
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
- 1,105
2
votes
2
answers
567
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 ...
- 1,314
2
votes
1
answer
418
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 ...
- 283
2
votes
1
answer
100
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:
...
- 282
4
votes
1
answer
818
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 ...
- 563
1
vote
0
answers
329
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 <...
- 631
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:
...
- 1,427
6
votes
3
answers
430
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
...
- 1,783
6
votes
1
answer
214
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 ...
- 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
...
- 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 ...
- 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 ...
- 3,100
4
votes
2
answers
302
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 ...
- 754
7
votes
6
answers
2k
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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.
- 2,324
2
votes
1
answer
542
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:
...
- 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 ...
- 13.8k
0
votes
2
answers
446
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 ...
- 2,324
2
votes
2
answers
702
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 ...
- 1,784
2
votes
2
answers
3k
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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?
- 33
9
votes
2
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2k
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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 ...
- 1,022
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:
...
- 1,681
1
vote
1
answer
144
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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.
...
- 1,783
3
votes
1
answer
743
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 ...
- 465
6
votes
4
answers
975
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 (<...
8
votes
5
answers
3k
views
Merging bed records based on name
I generated a file starting with the following bed lines:
...
- 3,100