HTSeq

HTSeq is a tool for the analysis of high-throughput sequencing data. It processes reads aligned with HISTAT or STAR and assign expression value counts. The HTSeq is also suitable for the quantification of single-cell RNA-seq data (scRNA-seq). The package also includes a htseq-count tool for pre-processing RNA-seq reads before differential expression analysis and a htseq-qa tool that assesses the read quality.