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• Sort a bed file
  Hi I tried to sort a bed file using *bedtools*. It sorted the chromosomes in, chr1 chr...
• Can't sort gff file ordered by chromosome (ch1,chr2,chr3......chrX).
  Dear all, I am trying to sort my gff file as ascending order by chromosome (chr1, chr2. chr3.......
• Reordering Bam files based on chromosome number, when the chromosome format is chr1..etc
  When trying to call variants I get the error message: ##### ERROR MESSAGE: Lexicographically...
• Bed File Coordinates
  Hi all, In a spreadsheet i have my list of rs# with their chromosomal number and locations. I wan...
• How can I bin my bed files into 500bp bins?
  I have several hundred bed files that will be processed by another colleague. I have been search...
• Average PhastCon score using bedops
  I want to uss bedops to some peaks' average phastCon score, and I followed this https://www.biost...
• Split bed file per sequence length
  I need to split my bed file into files with the same sequence length, but my original input file ...
• How to make single bam file from splited bam files
  Hi All, I have bam file splitted into all 23 chromosome(chr1.bam .... chr23.bam) for 1 sample....
• Replacing the Chr names and position notions in vcf
  Dear All I have a combined VCF file of few individuals. In this VCF instead of having normal CHR1...
• awk one line command
  I want to break my bed file into the chromosome-specific files containing the data of respective ...
• Merge overlapping and adjacent features in the BED file having the same label in the name (4-th) column
  Hi there! My `BED` file looks like: chr1 10 20 A chr1 15 20 B chr1 19...
• [Resolved] Extract Top score peaks from a .bed
  Hello, I have troubles extracting the best score peaks from my bed file. I have something like ...
• bedtools_intersect files sorting problem
  Dear all, I am running the command: bedtools intersect -sorted -g [GENOME_FILE] -abam [BAM_FILE] ...
• bedtools merge with strandedness giving now output
  Hello, I have a bed file and need to merge with strand specificity, but I am not getting an outpu...
• Plot multiple bed files using R package Gviz
  Hi, I am new to R and looking for some help in plotting multiple bed files which may or may not o...
• How Many Reads In A Bam File Are Aligned To a Specific Region
  I have BAM files from Hi-C experiment. I'd like to know how many of my aligned reads fall in a pa...
• bedtools merge, ERROR: file has non positional records, which are only valid for the groupBy tool.
  I am attempting to utilize `bedtools merge` (which I have used many times before), to merge overl...
• Merging Bam Files With Different Headers
  This might be a trivial question, but I would rather ask then make a mistake. What is the easies...