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• Looping bedtools multicov on paired bam and bed files
  Hi guys, I would like to run bedtools multicov on paired (by name) .bam files and .bed files. I...
• Bedtools multicover how to submit a bam list
  Hi, I'm trying to use bedtools muticov to find out Copy Number Variations among my samples, usi...
• how to use bedtools multicov
  I want to use bedtools multicov to handle with .bam(10X scRNA-seq) files ,but the data belongs to...
• Using Gnu Parallel For Bedtools
  I am trying to run gnu:parallel on bedtools multicov function where the original command is bed...
• bedtools multicov and fraction overlap flag
  I am trying to use bedtools multicov to count the reads that map to introns. For this I have cons...
• bedtools multicov problem
  bedtools multicov problems: I am counting number of mapped reads by using bedtools multicov: be...
• what does the bed file in bedtools multicov command refer to ?
  Dear bedtools users, Hope everything is well with you I want to use multicov mode to get rea...
• Bedtools Multicov Need A Bam Index File Specification Option
  bedtools version 2.16.2 multicov used to compute the multiple sample coverage given a feature fil...
• coordinate of BAM and BED
  Hi all, I want to use `bedtools multicov` to count the RNAseq reads in specific bed file interval...
• Should I filter my reads before running bedtools multicov ?
  Hi all: I am working on pair-end RNA-seq data to get read counts by running "bedtools multicov" ...
• how to calculate coverage in bam file over a specific bed file
  Hi every body, I have bam files (in different conditions) and a bed file with specific genes of ...
• bedtools multicov not running
  Hi guys, I'm trying to count the number of reads per gene (RNA Seq analysis) to perform the gene...
• average coverage, chip-seq
  Hi I need to determine average coverage in ChiP-seq peaks. I tried to use bedtools multicov with...
• get a bed file from a blast result
  Hi everyone I want to obtain a bed file from a blast result to as annotation to use in a bedtool...
• bedtools error: could not find indexes
  I want to use bedtools to count reads mapping back to genes, ultimately to use for differential e...
• bedtools multicov displays only the last BED feature
  I want to count the number of reads that fall in some predefined regions of a genome. Normally, t...
• Identify genes in a tophat aligned bam/sam file
  Hello all. I have sam/bam files with reads mapped to human genome from a RNA-seq experiment. I al...