Questions tagged [bedtools]
20 questions
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Obtain fraction of gene covered from bam file using bed file
I am trying to calculate the gene coverage of specific genes in a BAM file. I have a list of genes with thier start and end positions in a BED file. I would essentially like to know the number of overlaps for each gene and how well it is covered.
My…
Anuradha Ravi
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RStudio Server from Windows Subsystem for Linux cannot find packages on PATH
I am trying to use RStudio Server to run a package (CNV-CLinViewer) through Windows Subsystem for Linux.
All R packages required could be installed except for bedtoolsr, which requires bedtools (not an R package). I have bedtools installed on my WSL…
jordimaggi
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How to generate a custom bed file to use for bedtools intersect?
I have a custom reference genome, gene.fa and 18 bed files. I want to generate a bed file that contains a region of interest, 5100-5600 bp, as a single entry that I can use for intersection using bedtools intersect on my 18 bed files.
I was thinking…
Cam
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Using pybedtools with a BEDTools static binary
I want to use pybedtools in a python program that I am compiling into an executable with pyinstaller. The intent is that this executable will contain all of the necessary files to run the program, including shipping BEDtools as a binary. However,…
EggsandBakins
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Use a variable instead of a file for bedtools getfasta BED input?
I would like to input a variable in the place of a file in the command below, is this possible?
I would like to generate some FASTA files using the programme bedtools getfasta. Typically I would order the input files first using the awk to bedtools…
Jpike
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