K562.r1l1


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 <code>scanBam</code> from package <code>Rsamtools</code>.
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 <code>data(hg19DB)</code>.


datasets

Infer alternative splicing from paired-end RNA-seq data.
The model is based on counting paths across exons, rather than
pairwise exon connections, and estimates the fragment size and
start distributions non-parametrically, which improves
estimation precision.

David Rossell

casper

Characterization of Alternative Splicing based on Paired-End
Reads

K562.r1l1 function

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

Format

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

Source

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 <code>scanBam</code> from package <code>Rsamtools</code>.
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 <code>data(hg19DB)</code>.

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

Description

Usage

Arguments

Format

Source

References

Examples