It carries out precise and accurate read assignments by taking care of indels, junctions and structural variants in the reads
It takes only half a minute to summarize 20 million reads(真是快。。。)
It supports GTF and SAF format annotation
It supports strand-specific read counting
It can count reads at feature (eg. exon) or meta-feature (eg. gene) level
Highly flexible in counting multi-mapping and multi-overlapping reads. Such reads can be excluded, fully counted or fractionally counted(这点跟HTSeq-count不一样了,其对于多重比对的reads并不是只采用全部丢弃的策略,按照其说法是更加灵活的对待)
It gives users full control on the summarization of paired-end reads, including allowing them to check if both ends are mapped and/or if the fragment length falls within the specified range(可让使用者更加个性化的使用)
Reduce ambuiguity in assigning read pairs by searching features that overlap with both reads from the pair
It allows users to specify whether chimeric fragments should be counted(考虑的有点周到)
Automatically detect input format (SAM or BAM)
Automatically sort paired-end reads. Users can provide either location-sorted or namesorted bams files to featureCounts. Read sorting is implemented on the fly and it only incurs minimal time cost