featureCounts : limits on multioverlap (option -O)
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Last seen 3.9 years ago

Hello everybody (maybe it's not the good place for this question),

I'm running featureCounts (version 1.6.0, C code) with an annotation in SAF format, this way :

/home/marc/Downloads/subread-1.6.0-Linux-x86_64/bin/featureCounts -F SAF -L -T 3 -O -a saf.test -o /home/marc/Desktop/test_result exon.bam promoter.bam intron.bam five_prime_utr.bam three_prime_utr.bam intergenic.bam

saf.test contains for the 1st run, 50 features, all intentionally on the same region, with the same start & end (overlapping features). The reads were assigned as expected (all the 50 features have the same number of reads).

I have done this test in increasing the number of features, and I saw that for a number of 5000 overlapping features for example, no reads were assigned at all, even though on the screen, I can see it is said that the reads were assigned.

I'm doing these tests, because I want to replace an other tool by featureCounts because of its high speed, and I want to be sure it is free of unexpected results.

So, my question is the following : is there a limit in the number of handled overlapping features by the program ?

Thanks in advance !

Best regards,


featurecounts read counting • 590 views
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Last seen 11 minutes ago
WEHI, Melbourne, Australia

No, as you suspect, this isn't the right place to ask questions about the featureCounts command line version. This site for questions about Bioconductor software, so you could ask questions about the Rsubread package. Questions about Subread and featureCounts for the Unix command line should be sent to the subread Google group:


I can tell you though that there is no limit on the number of overlapping features. 5000 such features would be no problem in the slightest.


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