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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2
votes
3answers
81 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 ...
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0answers
31 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
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2answers
176 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
vote
1answer
77 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
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1answer
38 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
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0answers
298 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
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0answers
170 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 <...
2
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5answers
2k views

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

I have some problems with creating a .bed file for hg19 which I will be able to load on IGV. The fasta file contains rows of this form: ...
0
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0answers
46 views

From bedtools “genomecov” back to .bed

I have the results of: bedtools genomecov -d... Output: 0 0 10 10 10 20 20 And i want to convert it back to bed file. e....
6
votes
3answers
224 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 ...
6
votes
1answer
108 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
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1answer
45 views

How to apply function on bedfile based on a reference bedfile

I have two bed-like files: File1 ...
2
votes
1answer
575 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 ...
5
votes
2answers
564 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
149 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 ...
7
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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.
2
votes
1answer
348 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: ...
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
266 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
289 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 ...
2
votes
2answers
1k 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?
8
votes
2answers
1k 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 ...
7
votes
2answers
103 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
1answer
102 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
1answer
338 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 ...
6
votes
4answers
384 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 (<...
6
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5answers
2k views

Merging bed records based on name

I generated a file starting with the following bed lines: ...
11
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4answers
3k 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, ...
6
votes
3answers
711 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 ...
11
votes
3answers
6k 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 - ...
5
votes
4answers
777 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 ...
4
votes
2answers
190 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
203 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 ...
6
votes
1answer
54 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 ...
6
votes
1answer
403 views

How to filter out cross alignments from a BED file?

I have a BAM file: ...
17
votes
7answers
7k views

How to convert FASTA to BED

I have a FASTA file: ...
16
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3answers
2k 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 ...