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Subread 2.0.2 is a minor upgrade from the 2.0.1 version. The new version is mainly for bug fixing. The only change to the behaviour of the programs is the "--countReadPairs" parameter of featureCounts. Now users need to specify the "-p" option if paired-end SAM or BAM files are provided as input, then specify the "--countReadPairs" option if counts of read-pairs, instead of reads, are intended.