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8	"Data and information management is..." Data and information management is slowly moving out of infancy in genomics science…. at the toddler stage… The Good news Some data formats are being accepted widely The Bad news Still many competing standards in some areas Interoperability of data standards is almost non-existent Governance is questionable
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10	Data Format Types Raw Sequence Data e.g. fasta Aligned data e.g. BAM Processed data e.g. BED
11	Interpreting raw data
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14	HTseq Raw Data Format fasta (Sanger) csfasta (SOLiD) fastq (Solexa) sff (454) …. And about 30 other file formats http://emboss.sourceforge.net/docs/themes/SequenceFormats.html
15	SOLiD Color Space
16	(cs)Fasta/(cs)Fastq FASTA Header line “>” Sequence FASTQ Add QVs encoded as single byte ASCII codes Most aligners accept FASTA/Q as input Issue: data is volumous (2 bytes per base for FASTQ) Do PHRED scaled values provide the most information?
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27	454 output formats
28	Illumina output formats
29	"ASCII value for h" ASCII value for h= 103 Quality of Base A at the position 1 = 103- 64 103- 64 = 39 Where 39 is the phred score
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32	NGS QC Toolkit & FastQC
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