HTSeq: Analysing high-throughput sequencing data with Python

• Overview
  • Authors
  • Citation
  • Documentation overview
  • License
• Prequisites and installation
  • Installation on Linux
  • Installation on MacOS X
  • MS Windows
• A tour through HTSeq
  • Reading in reads
  • Reading and writing BAM files
  • Genomic intervals and genomic arrays
  • Counting reads by genes
  • And much more
• A detailed use case: Transcription start sites
  • Using the full coverage
  • Using indexed BAM files
  • Streaming through all reads
• Counting reads
  • Preparing the feature array
  • Counting ungapped single-end reads
  • Counting gapped single-end reads
• Reference overview
  • Parser and record classes
  • Specifying genomic positions and intervals
  • Genomic arrays
  • Special features for SAM/BAM files
• Sequences and FASTA/FASTQ files
  • Sequence
  • SequenceWithQualities
  • FastaReader
  • FastqReader
• Genomic intervals and genomic arrays
  • GenomicInterval
  • GenomicPosition
  • GenomicArray
  • GenomicArrayOfSets
  • Negative Index
• Read alignments
  • Concepts
  • Parser classes
  • Alignment and AlignmentWithSequenceReversal
  • Format-specific Alignment classes
  • Multiple alignments
  • CIGAR strings
• Features
  • GFF_Reader and GenomicFeature
• Other parsers
  • VCF_Reader and VariantCall
  • Wiggle Reader
  • BED Reader
• Miscellaneous
  • FileOrSequence
  • Version
• Quality Assessment with htseq-qa
  • Plot
  • Usage
• Counting reads in features with htseq-count
  • Usage
• Version history
  • Next version (current master)
  • Version 0.13.5
  • Version 0.12.4
  • Version 0.12.3
  • Version 0.11.4
  • Version 0.11.3
  • Version 0.11.2
  • Version 0.11.1
  • Version 0.11.0
  • Version 0.10.0
  • Version 0.9.1
  • Version 0.9.0
  • Version 0.8.0
  • Version 0.7.2
  • Version 0.7.1
  • Version 0.7.0
  • Version 0.6.1
  • Version 0.6.0
  • Version 0.5.4
  • Version 0.5.3
  • Version 0.5.2
  • Version 0.5.1
  • Version 0.5.0
  • Version 0.4.7
  • Version 0.4.6
  • Version 0.4.5
  • Version 0.4.4
  • Version 0.4.3
  • Version 0.4.2
  • Version 0.4.1
  • Version 0.4.0
  • Version 0.3.7
• Notes for Contributors
  • Source code
  • Languages
  • Build process
  • Distributing
  • Files

• Index