RnaSeqTutorial: An RNA-Seq tutorial

In UPSCb/RnaSeqTutorial: RNA-Seq Tutorial

Description

This tutorial, described in the attached RnaSeqTutorial vignette, introduces the core Bioconductor packages necessary for processing RNA sequencing data. It then introduces the easyRNAseq package that can simplify this task and offer different processing to be done one Next-Generation Sequencing data. It was used for various Bioconductor workshops since June 2010.

Arguments

RnaSeqTutorial

The vignette containing the tutorial.

Format

The different data available are:

• in data:

  • gAnnot A file containing the Drosophila melanogaster genic annotation retrieved from FlyBase v5.29 (June 2010) and converted into a RangedData object. Although the corresponding gff file has been deprecated - see below - that annotation is still usable.

  • gRngList A file containing the Drosophila melanogaster mRNA and exon annotation retrieved from FlyBase v5.52 (April 2013) and converted into a GRangesList object.

• in extdata:

  • ACACTG.bam, ACACTG.bam, ATGGCT.bam, TTGCGA.bam 4 RNA-Seq samples from D. melanogaster demultiplexed, with their associated .bai indexes

  • Dmel-mRNA-exon-r5.52.gff3 The gff3 file containing the information stored in the gRngList GRangesList object mentioned above.

  • annot.gff Deprecated. The gff file containing the information stored in the gAnnot RangedData object mentioned above.

  • gapped.bam A D.melanogaster RNA-Seq file containing a few examples of gapped alignment (done by tophat) surrounding the Mef2 gene locus

  • multiplex_export.txt.gz The original export file containing the multiplexed data mentioned above.

  • subset_export.txt.gz A D.melanogaster RNA-Seq export file, restricted to 100,000 reads

  • subset.bam The same aligned against the reference genome (D.melanogaster v3).

Value

Some fantastic knowledge.

Examples

	## Not run: vignette("RnaSeqTutorial")

UPSCb/RnaSeqTutorial documentation built on Nov. 24, 2020, 12:40 a.m.