K562.r1l1: Toy RNA-seq data from RGASP project.

In casper: Characterization of Alternative Splicing based on Paired-End Reads

Description

The paired-end RNA-seq data is from the RGASP project sample K562_2x75 (replicate 1, lane 1) and was obtained at ftp://ftp.sanger.ac.uk/pub/gencode/rgasp/RGASP1/inputdata/human_fastq. Reads were aligned against hg19 with tophat 2.0.2 and bowtie 0.12.5, setting the insert size at -r 200, and imported into R using scanBam from package Rsamtools. For illustration purposes, we selected reads mapping to a few genes only (namely, the genes that were also selected for the toy genome annotation in data(hg19DB).

Usage

data(K562.r1l1)

Format

A list indicating read id, chromosome, start and end locations and the position of the pair, as returned by scanBam.

Source

ftp://ftp.sanger.ac.uk/pub/gencode/rgasp/RGASP1/inputdata/human_fastq

References

C Trapnell, L Pachter, SL Salzberg. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 2009, 25, 1105-1111. doi=10.1093/bioinformatics/btp120.

B Langmead, C Trapnell, M Pop, SL Salzberg. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 2009, 10:R25.

Examples

data(K562.r1l1)
names(K562.r1l1)

casper documentation built on Dec. 17, 2020, 2:01 a.m.