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• How can get overlap size in bedtools multi-intersect?
  Hi, I have 4 files I'd like to intersect but I need to know the size of the overlap I can get it...
• BedTools intersect - Segmentation fault
  Hi, Has anyone experienced the "segmentation fault" error while trying to use bedtools intersect...
• How To Merge Isoforms For A Gene
  Hi All, I want to ask a tech question. Does anybody have scripts or software that can merge mult...
• Bedtools intersect -u or -wa causing issues
  I'm trying to intersect two tracks and only keep the transcripts from input a that overlap with i...
• Bedtools intersect returns 0, intersections present on IGV
  Hello, I am trying to use bedtools to find intersections between H3K4me1 peaks and my regions o...
• bedtools intersect + subtract not adding up to original file?
  Hi, I have a BED file of features in the genome, for which I am trying to see how many bases ove...
• Get nonoverlapping regions of two bed files
  I have two bed files. I want to find the regions of non-overlap between the two; for example, I h...
• 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...
• "mask" values in a bedgraph
  I am trying to plot average conservation in a list of genomic features, and so far managed to do ...
• Bedtools intersect with minimum overlap required as a number
  Hello all. I have 3 column bed files (chrom, chromStart, chromEnd). I am looking to run bedtools...
• bedtools intersect -c flag output
  I have been using BEDtools intersect to determine on-target proportions of reads from BAM files i...
• Finding Overlapping Variants (I.E. Indels, Snps) Using Annovar Format.
  Hello, I know that using bedtools functions (specifically intersect and windows), it is possible...
• Can genomicranges do bedtools-like intersection operations?
  In bedtools intersect means "for each read in A, for each read in B that overlaps, find the part ...
• Intersect Gene Annotation With Specific Position Or Genomic Interval
  Hi, I've several genomic interval and I want to check if they are overlapping with known gene. I...
• Stats on the overlapping length within two bed files
  Hi all, I have two bed files, and I have run bedtools intersect to calculate the overlapping re...
• Combining two databases in gtf file, bedtools gives wierd result
  I'm trying to put genes from ENCODE and NONCODE in one gtf file and filter out NONCODE genes whic...
• sort suitable overlap base by using bedtools intersect
  When I use bedtools intersect funtion how i can sort which have 10 bases or longer overlap in ove...
• bed file intersection overlapping regions in at least x files
  Hi, I have a set of 20 .bed files, now I want to compare them and create a novel .bed file that...
• Differential Isoform Expression In Cuffdiff: How Does It Work?
  I am running an analysis in CuffDiff using a GFF file of annotations from FlyBase (www.flybase.or...
• Bedtools Intersect with files containing some alternative information
  Do two files have to have the exact same information in them to intersect the two files? I'm tryi...