inst/extdata/README.md

In FRASER: Find RAre Splicing Events in RNA-Seq Data

Datasets accompanying the FRASER package

The FRASER packages contains an example dataset that is a subset of the Kremer et al study. The main purpose of those files are to demonstrate the functionality of the FRASER package.

BAM files

The three BAM files in inst/extdata/bam belong to one of the diagnost individuals from the study. In short, they contain Illumina RNA-seq data from fibroblast samples and aligned with STAR against the UCSC hg19 assembly. For this package only reads spanning the genes MCOLN1 and TIMMDC1 are extracted. More details on the protocol can be found in the Method section.

Count matrices

The split-read and splice-site-read count matrices (inst/extdata/raw_junction_counts.tsv.gz and inst/extdata/raw_site_counts.tsv.gz) are also a subset of the Kremer et al study. Here, the individuals with diagnosed splice defects and some controls are picked. The counts are extracted from the BAM files with the function FRASER::countRNAData. Again it contains only a subset of count for the genes TIMMDC1 and MCOLN1.

Sample annotation

Both datasets are accompanied by a pseudo anonymised sample annotation.

FRASER documentation built on Feb. 3, 2021, 2:01 a.m.