Questions tagged [bedtools]

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bedtools coverage - Report the depth at each position in each A feature

I am using bedtools coverage to compute the sequencing depth at every positions of a chromosome but it didn't work as I expected. Instead it reported 0 coverage at every positions. This is how I did ...
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bedtools single-nucleotide coverage in BED-specified regions for multiple BAMs

I have a BED6 (BED + name, score, strand info) file that defines some regions of interest. I also have a set of BAMs corresponding to different samples. I would like to obtain output similar to <...
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Question: Combine BedTools Closest and Window Command

I am new to using Bedtools so please excuse my possible naive question. Let's say my file A is Snps and file B is genes. The Closest command with -k flat let one set how many genes that are closest to ...
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multiBamCov for counting reads overlapping a bin interval

I am using multiBamCov from bedtools to count reads in my bed file. I want to count the reads in the specified bins in my bed file such that if the read in the bam file overlap the interval more than ...