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Questions tagged [bedtools]

20 questions
3
votes
1 answer

Find rows with overlapping ranges

I have 3 large data frames that look like this: library(tibble) df1 <- tibble(peak=c("peak1","peak2","peak3"), coord1=c(100,500,1000), coord2=c(250,700,1250)) df2 <- tibble(peak=c("peak5","peak6","peak7"), …
Corrector
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3
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1 answer

Filter overlapping entries in bed file

I have a bed file that looks like this: 1 183113 183114 chr1:183113-183240 0 + 1 187286 187287 chr1:187128-187287 0 - 1 187576 187587 chr1:187375-187577 0 - 1 187580 187590 chr1:187379-187577 0 - My aim is to extract…
maciek
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Different results with MACS2 when Peakcalling with .bed or .bam

I got the following problem: I use MACS2 (2.1.0.20140616) with the following short commandline: macs2 callpeak -t file.bam -f bam -g 650000000 -n Test -B --nomodel -q 0.01 It seems to work as I want, but when I convert the .bamfile into .bed via…
N. F.
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1 answer

Problems with bedtools installation

I am a very new beginner in bash programming and never succeed in installing tools on my computer. I am trying to install bedtools without any success I typed these following commands on my terminal wget…
Aurelia Kurtis
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1 answer

Parse out gene name after bed and vcf intersect

I'm looking for to add a new column of 'GENE_ID' to the vcf file based on an intersect between bed coordinate and vcf positions. The 'GENE_ID' is already present as the 4th column in the bed file. Basically I need to know how to keep that gene name…
Maya_Cent
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1 answer

bedtools shuffle -excl doesn't seem to warn about consistent naming convention

After using bedtools shuffle a lot with the -excl set on I noticed that the excluding file has the numeric naming convention whereas my input file has the "chr" naming convention. Does someone know if this will cause any problems? I have generated…
user2449089
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1 answer

pybedtools bam_to_bed() bedpe

I'm feeling dumb, but I can't figure out the syntax below, and I've been googling the w/o success for a while. Very easy, I have a bam I want to convert to bedpe with pybedtools within a script. The following works great: pybed_BAM =…
Matteo
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2 answers

is there an R function similar to bedtools intersect?

when working with bedtools intersect , there are many options that you could use like setting minimum overlap as percentage of file A or B , or whether to write original A or B entries. I was wondering if there is a package in R that does the same I…
pegahT
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1 answer

converting multiple BAM files to BED files

I have BAM files in the external hard drive. Want to convert them into BED. Am using cd /media/amit/LaCie/mdc_work/chigozie/pool1/bam for x in *.bam ; do echo "print current:$x"; bedtools bamToBed -i "$x" > "${x%.bam}.bed"; done echo…
user1738234
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1
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1 answer

Filter overlapping entries in bed file (2)

This is a follow-up of my previous question. This time, in case two entries in bed file overlap I would like to keep one of them in the output (randomly selected). Preferably, I look for a modification of the previous answer (bedtools package). For…
maciek
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1 answer

using perl array as input to bash bedtools command

I'm wondering if it is possible to use a perl array as the input to a program called bedtools ( http://bedtools.readthedocs.org/en/latest/ ) The array is itself generated by bedtools via the backticks method in perl. When I try to use the…
furryfoo
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0
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1 answer

ISSUE: malformed BED entry at line 2. Start was greater than end. Exiting. bedtools

I am trying to use bedtools getfasta on a txt file but some of the chromosome coordinates from big to low, how can I fix this so that all chromosome coordinates are from low to big? I am using command line on Ubuntu. I expected the command to run…
Deep
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Installing Deeptools in R

> install.packages("bedtools") Also tried this with bedtoolsr. Is there a way to force install? I am using version R 4.2.2. Warning in install.packages : package ‘bedtools’ is not available for this version of R A version of this package for…
erman
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1 answer

bash loop file in one folder against all files in another folder

I am trying to do a (bedtools) intersect. Anyone see what is wrong with my bash code here? #!/bin/bash dir=$(pwd) query=$dir/query_beds pgs=$dir/pgs_beds for file in $query/*; do bedtools intersect -wa -wb -a $file -b $pgs/* -c -C -sorted…
clemaster
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Getting tsv file into 1Kb genomic bins

I have a .tsv file set out as chromosome - genomic position - methylation status: I want to bin it into 1Kb bins of genomic regions, as well as get the third columns average.enter image description here i.e. Get the methylation average per 1kb…
Hannaho
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