How does it compare to HTSeq?
A Python library to facilitate the rapid development of such scripts. HTSeq offers...classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. The researchers also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes (Source: http://www.rna-seqblog.com/htseq-a-python-framework-to-work-with-high-throughput-sequencing-data/)
Cufflinks estimates expression profiles using a statistical model in which the probability of observing each fragment is a linear function of the expression level of the transcripts from which it could have originated....HTSeq uses a naive count-based approach for expression estimation. The htseq-count script allows the user to choose how reads assigned to the corresponding gene from a list of three modes. These modes correspond to the overlap of features in the alignment:“union”, “intersection-strict”, and “intersection-nonempty”. (Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003039/)