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• What exactly does the -fs flag (fragment size) do in bedtools genomecov/genomeCoverageBed?
  I am trying to extract per-base read mapping coverage from a BAM file based on several regions of...
• bedtools genomecov -bg -split -ibam bamfile. error: the input file is not sorted correctly.
  Hi there, I try to run command "**bedtools genomecov -bg -split -ibam bamfile**" to obtain the b...
• Bedtools genomecov to identify regions at any coverage
  Hi,   Is it possible to use bedtools genomecov with both -bga and -max flags? I've been trying...
• How to split genome coverage by read length in Ribo-Seq data
  I am looking for an efficient/simple way for extracting genome coverage for each strand(+/- ) in ...
• coverage on exons with bedtools genomecov
  Hello everyone, I would like to have per-base coverage of a bam file of an RNAseq experiment, bu...
• Genomecov 0 or 1 based results?
  Hi all, From what I understand BED and BAM format are 0-based (but BED is exclusive on the stop)...
• localised drops in read depth across sam/bam
  Hi I have been visualising number of alignments to each nucleotide using a depth file generated ...
• bedtools genomecov per-base report in igv
  Hi All, Is there a way to transform the per-base report of an alignment file into igv-readable f...
• Genomecov -scale flag usage
  I am trying to use bedrolls genomecov in order to scale my RNA seq data to reads per million. I ...
• compute genome coverage from specific bam contig
  Hi there, I have a BAM file containing mutliple contigs. I want to compute coverage only on a sp...
• bedtools genomecov produces negative coverage.
  Hi, I'm trying to compute fragment coverage from paired-end (50x2) RNA-seq data using [bedtools g...
• Converting Bedgraph to coverage
  I downloaded a dataset from your the UCSC Genome Browser- "Table Browser" with the following inpu...
• Plotting large file size of bedtools genomecov output
  Hi everyone, I generated the output for coverage using bedrolls genomecov using this command: ...