bedtools2
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arq5x
bedtools - the swiss army knife for genome arithmetic
Hi, I have the following regions in a bed file called `example.bed`: ``` chr1 11675 11677 chr1 11780 15264 chr1 15355 15797 ``` Now I would like to make windows...
Heys, I am having problems when trying to calculate coverage levels of a bed file with genomeCoverageBed (v2.3), as my bam and bed files are sorted differently: cut -f 1...
Hi, I am using pybedtools (0.8.1) coverage to count the features spanning the interval, and I want to filter the features whose overlap don't satisfy the fraction required for A...
Currently, even with sorted data, the algorithm is two-pass. It can reallty be done in one pass. As such, memory and runtime will be reduced.
Hi, Thank you for the creation and maintenance of bedtools. It's hard for me to comprehend the results of using " bedtools fisher" to calculate the overlapping of two bed...
Hello, Related to #866, we have a specific sample where `bamtofastq` outputs empty reads at the beginning of `fq1` and `fq2` before printing out the rest of the reads. I...
command: `bedtools genomecov -d -g genome.size -ibam in.bam > out.cov` _genome.size_ consists of a single RNA "myRNA", length = 8 kb nucleotides. _in.bam_ contains > 15 million reads aligned to...
bamtobed adds an additional entry that does not exists in the BAM file. This seems to occur when the last read is unpaired and the previous read is paired in...
Many thanks for keeping the powerful bedtools up to date The -is option for pairToPair latest documentation [here](https://bedtools.readthedocs.io/en/latest/content/tools/pairtopair.html) specifies that it is for forcing strandedness. In my tests it actually...
I was trying to get the unmapped reads from a bam file and convert it to a interleaved fastq file by `bamToFastq` but having a unexpected behavior. According to the...
