Bioconductor packages for short read analysis - Details

In this lecture, Nicolas Delhomme describes in detail the Bioconductor packages that can be used for the analysis of short reads.

Particular emphasis is put on the following packages:

  • ShortRead and Rsamtools for file I/O, quality assessment, and high-level, general purpose data summary.
  • IRanges and GenomicRanges for range-based (e.g., chromosomal regions) calculation, data manipulation, and general-purpose data representation.
  • GenomicFeatures for annotation of sequence features across common genomes.
  • BSgenome for accessing and manipulating curated whole-genome representations.
  • Biostrings for alignment, pattern matching (e.g., primer removal), and data manipulation of large biological sequences or sets of sequences.
  • rtracklayer for import and export of tracks on the UCSC genome browser.
  • biomaRt for access to Biomart databases.
Notes

The code used by Nicolas during this lecture can be found here

This lecture was followed by a practical; the handout for the practical can be found here, along with the code and two additional packages developed by Nicolas for this course, easyRNASeq and RnaSeqTutorial.

In order to follow this practical you will need to install some of the following Bioconductor packages in your R session.

Please refer to the practical handout to identify the packages that you will need.