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  1. Organising your work Dr Konrad Paszkiewicz University of Exeter

  2. Analysis • Includes many steps • Which leads to many intermediate files

  3. Analysis • Includes many steps • Which leads to many intermediate files • Important to document what you do as you do it • Organise your folders and file naming • Enables clear audit trail • Easy to check parameters

  4. Analysis • Includes many steps • Which leads to many intermediate files • Important to document what you do as you do it • Organise your folders and file naming • Enables clear audit trail • Easy to check which parameters were used

  5. Example Project Arabidopsis Bra1/ Comparison/ Sample Bra1 A/ Sample Bra1 B/ Bra1A vs Bra1B/ raw_illumina_reads/ remapping to reference/ denovo assembly/ SNP calls/ annotation/ SNPs PFAM domains reference_genome/

  6. Summary files • In each Project directory create a file explaining what the project aims are and details of the sequencing run • In each Sample directory create a text file explaining what the sample is

  7. History command • The ‘history’ command on your terminal lists all the commands you have typed in • history > my_record.txt • Put one in each of your directories as you complete each analysis

  8. History