RNA sequencing is performed on all HipSci iPS cell lines that are selected for banking after passing QC. Sequencing and primary analysis are performed at the Wellcome Trust Sanger Institue.
HipSci’s RNA-seq analysis pipeline is to map sequence reads to the human GRCh37 reference using the STAR spliced aligner. The mapping uses version 19 of the Gencode gene annotation to enable splice-aware alignments.
Getting the data
- Raw sequencing reads – Distributed in the cram file format. Any cell line can have multiple associated cram files; each corresponds to a single lane of sequencing.
- Splice-aware STAR alignment – Distributed in the bam file format. We distribute one bam file per cell line.
HipSci’s FTP site contains: