Reproducibility

Learning outcomes

After having completed this chapter you will be able to:

Understand the importance of reproducibility
Apply some basic rules to support reproducibilty in computational research

Material

Some good practices for reproducibility

During today and tomorrow we will work with a small E. coli dataset to practice quality control, alignment and alignment filtering. You can consider this as a small project. During the exercise you will be guided to adhere to the following basic principles for reproducibility:

Execute the commands from a script in order to be able to trace back your steps
Number scripts based on their order of execution (e.g. 01_download_reads.sh)
Give your scripts a descriptive and active name, e.g. 06_build_bowtie_index.sh
Make your scripts specific, i.e. do not combine many different commands in the same script
Refer to directories and variables at the beginning of the script

By adhering to these simple principles it will be relatively straightforward to re-do your analysis steps only based on the scripts, and will get you started to adhere to the Ten Simple Rules for Reproducible Computational Research.

By the end of day 2 ~/project should look (something) like this:

.
├── alignment_output
├── reads
├── ref_genome
├── scripts
│   ├── 01_download_reads.sh
│   ├── 02_run_fastqc.sh
│   ├── 03_trim_reads.sh
│   ├── 04_run_fastqc_trimmed.sh
│   ├── 05_download_ecoli_reference.sh
│   ├── 06_build_bowtie_index.sh
│   ├── 07_align_reads.sh
│   ├── 08_compress_sort.sh
│   ├── 09_extract_unmapped.sh
│   ├── 10_extract_region.sh
│   └── 11_align_sort.sh
└── trimmed_data