| Uses the htseq-count script from the Python HTSeq package. Given a file with aligned sequencing reads and a list of genomic features, count how many reads map to each feature. A feature is defined as an interval (i.e., a range of positions) on a chromosome or a union of such intervals. In the case of RNA-Seq, the features are typically genes, where each gene is defined as the union of all it's exons. One may also consider each exon as a feature, e.g., in order to check for alternative splicing. For comparative ChIP-Seq, the features might be binding regions from a pre-determined list. |
hg clone https://toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count