| 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
| Name | Version | Type | |
|---|---|---|---|
| htseq | 0.6.1 | package | |
| numpy | 1.7.1 | package | |
| pysam | 0.7.7 | package | |
| samtools | 0.1.19 | package | |
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| - Count aligned reads in a BAM file that overlap features in a GFF file | 0.6.1galaxy1 | any | |