Tutorials

This page contains a few tutorials to help you familiarize yourself with HTSeq, including htseq-count and its barcode sibiling htseq-count-barcodes.

Parsers

• Tutorial: Using Fasta/Fastq parsers: Simple tutorial on hadling fasta and fastq files with HTSeq.
• Tutorial: Using the SAM/BAM/CRAM parsers: Simple tutorial on handling SAM/BAM/CRAM files.
• Tutorial: StepVector versus StretchVector: Explanation of the different data structures used to store sparse genomic data.

Workflows

• Tutorial: Transcription start sites (TSS): TSS example for the HTSeq API
• Tutorial: High C data exploration: Chromatin conformation example for the HTSeq API

Scripts

• Opening the black box of htseq-count: Explanation of the inner workings of htseq-count
• Quantifying exon-level expression with htseq-count: Calling htseq-count at the exon level.