test_dataset.rst

Demo dataset

We have put together a small demo dataset that is used in the tour and in examples. It consists of feature annotations, ribosome profiling data, and RNA-seq from the merlin (laboratory) strain of human cytomegalovirus (hCMV).

Downloads:

• demo dataset part one, for all of the tutorials
• demo dataset part two, specifically used in /examples/gene_expression.

Part 1 includes the following files:

Filename	Contents	Source
merlin_NC006273-2.fa	Sequence of hCMV merlin strain	GenBank, accession no. NC_006273.2
merlin_orfs.bed, merlin_orfs.gtf	Coding region models for hCMV strain, plus estimated UTRs	Stern-Ginossar2012 (CDS). 5' UTRs estimated as 50 nt upstream of CDS. 3' UTRs estimated as 100 nt downstream of CDS.
SRR609197_riboprofile_5hr_rep1.bam	Ribosome profiling data, 5 hours post hCMV infection, aligned to hCMV merlin strain genome sequence	Stern-Ginossar2012, raw data available at SRA, accession no. SRR609197
SRR592963_rnaseq_5hr_rep1.bam	RNA-seq data, 5 hours post CMV infection, aligned to hCMV merlin strain genome sequence	Stern-Ginossar2012, raw data available at SRA, accession no. SRR592963

Part 2 includes further replicates, as well as timepoint data from 24 hours post-infection.