bedtools
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arq5x
A powerful toolset for genome arithmetic.
I'm interested in defining column separator for -c option in bedtools merge. I have a bedj file where the 4th column of input file has characters that are automatically detected...
Dear friend, It's a kind reminder that the bedtools makewindows will not work for large genome size, like larger than 4.29Gb. Could you set the maximum size larger? The 4.29Gb...
Hi, I'm running `bamToBed` on an RNA-seq `bam` file with the `-splitD` argument in order to view each aligned segment in a different line in the `bed` file, but I...
Hi, thanks again for providing this amazing toolkit. The `fisher` command appears useful for checking the significance of overlap very quickly. But I wonder whether there is a bit more...
I installed pybedtools 0.8.0 ################################ import pybedtools a = pybedtools.example_bedtool('a.bed') b = pybedtools.example_bedtool('b.bed') a_and_b = a.intersect(b) ################################ ################################ It gives the response below: Traceback (most recent call last): File "",...
I have a genomic region that have `chr, start and end` as a bed format. I have a gene annotation in bed format too. What is the best way to...
Hi, I want to get the coordinates of input file by extending 1000000bp up/downstream of TSS: cat input.csv | awk 'NR>1{print $1"\t"$5"\t"$6}' | bedtools window -b stdin -a genes.bed -w...
Hello everyone, I have a test.bed file with this structure: ``` chr4 74445406 74446534 AREG1 + chr4 74446782 74449047 AREG2 + chr20 57228229 57266628 BMP71 - chr20 57202475 57228421 BMP72...
It would be nice if `bedtools complement` accepted `-s`
