bedtools
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arq5x
A powerful toolset for genome arithmetic.
I noticed this when I had concatenated a fasta with DOS line endings (`0x0d 0x0a`) to a normal (Unix, `0x0a`) style fasta file. The Unix-style part of the file was...
I have a feature request: allow the `maskfasta`command to take `-` as the filename for both `-fi` and `-fo` to allow piping fasta files through maskfasta. So something like this...
Using coverage -c -s where -a is a bed file with strand info, and -b is a strand specific BAM alignment (RNA-seq in my case), I get very different values...
Hi... Is there a default 'GENOME' in bedToBam? Is it 'human.hg18.genome' or 'human.hg19.genome'? Or does it need to be specified always? Thanks much, George
Hi there Low priority request: https://bedtools.readthedocs.io/en/latest/content/installation.html ``` brew tap homebrew/science brew install bedtools ``` It looks like `brew tap homebrew/science` is no longer functional: ``` $ brew tap homebrew/science Error:...
please close. should have reported to pybedtools.
When I ran bedtools unionbedg -i 1.bg 2.bg -name 1 2> union.txt I got bedtools: unionBedGraphs.cpp:99: CHRPOS UnionBedGraphs::ConsumeNextCoordinate(): Assertion `!queue.empty()' failed. Aborted (core dumped) The bedtools is v2.25.0 The head...
Hi Maybe this is a silly question, but I recently found that `bedtools intersect` (v2.19.0) behaves weird when 0bp (those with identical start and end coordinates) features are compared. For...
help message shows that -5 mean "calculate coverage of 5' positions instead of entire interval", but I don't know what's 5' position exactly means? ZHANG Yan
Hello, I'm trying to filter out reads that map to a specific area using bowtie2 and bedtools intersect (moving reads not mapping to the region to a new file). This...
