Raw Reads

Raw read files (fastq) can be found on GEO (GSE86356).

Phenotypic Data

Patient phenotypic information will be hosted at dbGAP under controlled access. Investigators must apply for access to this information.

Mapped Reads

Mapped read files (bam) can be found below (PENDING). Reads were mapped using gsnap:

gsnap ...

Read Densities by Position

Bedgraph files can be found below. These files were generated from bam files using bedtools:

bedtools genomecov -ibam <bam> -g <genome> -bg -split > <bedgraph>
sort -k1,1 -k2,2n <bedgraph> > <sorted>
bgzip <sorted>
tabix -p bed <sorted.gz>

Gene Expression Estimates

Tables of gene expression estimates can be found below.

MISO Estimates

MISO estimates of isoform usage can be found below. MISO was run in single end mode, using the following parameters: