bedtools
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arq5x
A powerful toolset for genome arithmetic.
I would like to extract the centre of bed intervals by hijacking bedtools slop. A genome size file is unnecessary here since there is no way that an interval would...
In A.bed file I have: chr1 0 100 chr1 100 200 chr2 0 100 In B.bed file I have: chr1 10 20 chr1 20 30 chr1 30 40 chr1 100...
I have a sorted bam and a bed file and tried to find reads in the bam file that overlap with entries in the bed file. I tried two ways:...
Hi, I am having problem sorting files. I tried to sort bed file and bam file using sort -k1,1 -k2,2n. However, I keep on getting the error message. Could you...
my code: bedtools-2.25.0/bin/bedtools coverage -counts -sorted -a test.bed -b test.sort.bam the bed was sorted using : sort -k1,1 -k2,2n the BAM file ( after PE reads ) was sorted by...
The -sortout option for bedtools coverage is present at the manual web page (http://bedtools.readthedocs.io/en/latest/content/tools/coverage.html), however does not show up with bedtools coverage -h. Most importantly, bedtools coverage performs EXACTLY the...
Hi, Our team is trying to write code to parse through the bedtools documentation, and there are some bug/inconsistencies in the documentation that I think might need fixing. In "bedtools...
I'm using `bedtools intersect` (v2.27.1-1-gb87c465-dirty compiled from git latest source) on two bed filed that seem normal (http://paste.ubuntu.com/p/GxPWFb9Vby/ and http://paste.ubuntu.com/p/3Ndz5jkmrW/), and I get a strange error: ``` $ bedtools intersect...
Hi, I want to transform BAM(produced by Bowtie2) to BEDPE format. bam file was sorted by sequence names, and then do samtools view -f 0x2 -b test.srtn.bam | bamToBed -bedpe...
Hi, I created a bed file consisting of only exonic coordinates using GTFExtract (GTFUtils) which is a gtf information extraction tool and does not follow the 0 based coordinate system....
