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/ Sample Bra1 A/ Sample Bra1 B/ raw_illumina_reads/remapping to reference/ denovo assembly/SNP calls/annotation/ reference_genome/ Comparison/ Bra1A vs Bra1B/ SNPsPFAM domains

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