mapR00000173 contains the bamfiles and corresponding bamindexes generated by core. They have been mapped ONLY to R00000173.

The same applies to the QC's stored in P160016-QC

The fastq files are all stored here and need to be archived in due course.

maphuman contains the sam files and bam files (raw, sorted and index) from mapping the hs37d5 genome

mapnonhuman contains the sam and bam files mapped to a fasta file containing ERCC, plasmid and R00000173

Bamfiles from core mapped using Stampy but NOT mapped to any reference genome (dummy reference only)

HCV371 samples mapped using bwa-mem to /well/jknight/cyndi/metagenomics_data/P160016/reference_genomes/bwa1aHQall/ref.fasta ie. closest HCV reference genome (1a_HQ) + human + ERCC + plasmid