Dear Nicolas,
Many thanks for sending us your read data which helped us to identify the problem. The problem was that in your SAM file about half the fragments had their forward read appearing before their reverse read and the other half had their forward read appearing after their reverse read. This is not what featureCounts expects to see since most aligners always put the forward read before the reverse read in their mapping output.
The change of read order does not affect unstranded read counting with featureCounts, but it resulted in around half of the fragments not being counted when stranded read counting was performed, which is what you observed.
Nonetheless, we are now modifying featureCounts to deal with this situation and a patch will be released soon.
Best wishes,
Wei
Many thanks for sending us your read data which helped us to identify the problem. The problem was that in your SAM file about half the fragments had their forward read appearing before their reverse read and the other half had their forward read appearing after their reverse read. This is not what featureCounts expects to see since most aligners always put the forward read before the reverse read in their mapping output.
The change of read order does not affect unstranded read counting with featureCounts, but it resulted in around half of the fragments not being counted when stranded read counting was performed, which is what you observed.
Nonetheless, we are now modifying featureCounts to deal with this situation and a patch will be released soon.
Best wishes,
Wei
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