text: user1075: I am using featureCounts from the subread package to count the number of fragments per gene in an RNA-seq experiment. I feed it a BAM file with paired-end reads aligned to a reference genome. In the help page of the executable, which I have installed using conda install subread, there is a section about overlaps, including for example the -O option which will assign the reads/fragments to all overlapping features. What is the default behaviour? Assigning to reads/fragments to the feature with largest overlap? not assigning multi-overlapping reads/fragments?
  I would appreciate your help on this.
  OS: macOS X
  featureCounts version: 1.6.3
  
  user77: If a fragment overlaps multiple genomic features then it's unassignable, which is the appropriate way to handle ambiguous mappings when the resulting counts are then given to tools like DESeq2.
  
original_text: 1075: <p>I am using <a href="https://academic.oup.com/bioinformatics/article/30/7/923/232889" rel="nofollow noreferrer">featureCounts</a> from the subread package to count the number of fragments per gene in an RNA-seq experiment. I feed it a BAM file with paired-end reads aligned to a reference genome. In the help page of the executable, which I have installed using <code>conda install subread</code>, there is a section about overlaps, including for example the <code>-O</code> option which will assign the reads/fragments to all overlapping features. What is the default behaviour? Assigning to reads/fragments to the feature with largest overlap? not assigning multi-overlapping reads/fragments?</p>
  
  <p>I would appreciate your help on this.</p>
  
  <p>OS: macOS X</p>
  
  <p>featureCounts version: 1.6.3</p>
   77: <p>If a fragment overlaps multiple genomic features then it's unassignable, which is the appropriate way to handle ambiguous mappings when the resulting counts are then given to tools like DESeq2.</p>
  