Questions tagged [bed]
Browser Extensible Data, a collection of related plain text formats for describing genome features for visualization with genome browsers.
69
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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
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Where to find the homopolymer regions bed file for Hg002 genome?
This question was also asked on Biostars
I am doing an experiment where I am trying to analyze the errors in the homopolymer regions between the polished reference hg002 genome and hifiasm assembly ...
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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 ...
- 309
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How to add corresponding "chr" before location (start, end) of bed alike file?
I have some bed alike files but don't have chr term in the fisrt column, that I want to add chr and its corresponding chromosome ...
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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, ...
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644
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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?
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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 ...
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132
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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 ...
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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:
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3
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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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1
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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 ...
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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 ...
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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 ...
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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:
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- 31