<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>

CC BY-SA 4.0
2019-03-18T10:44:11.987Z
fair enough, so I will not use the -O option, thanks
Biomagician
CC BY-SA 4.0
2019-03-18T08:12:53.997Z
2019-03-18T08:12:53.997Z
Devon Ryan
<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>

<software-usage><subread><featurecounts>
How do I tell featureCounts to ignore fragments that overlap with more than one feature?
# How do I tell featureCounts to ignore fragments that overlap with more than one feature?

(Asked by: username_0 on 2019-03-18)

I am using [featureCounts](https://academic.oup.com/bioinformatics/article/30/7/923/232889) 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

**Tags:** software-usage, subread, featurecounts

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## 1 answers

### Answer by username_1 on 2019-03-18. Score: 1 | Accepted answer

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.

> **Comments:**
> **username_0**: fair enough, so I will not use the -O option, thanks  

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