Raw read files (fastq) can be found on GEO (GSE86356).
Patient phenotypic information will be hosted at dbGAP under controlled access. Investigators must apply for access to this information.
Mapped read files (bam) can be found below (PENDING). Reads were mapped using gsnap:
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>
tabix -p bed <sorted.gz>
Tables of gene expression estimates can be found below.
MISO estimates of isoform usage can be found below. MISO was run in single end mode, using the following parameters: