Butlin:Unix for Bioinformatics - advanced tutorial

Overview

This session will be more challenging if you are still new to Unix. However, it’s main aim is to demonstrate that Unix is much more than an environment in which you can execute big programmes like `bwa` or `samtools`. Rather, with it’s suite of text searching, extraction and manipulation programmes, it is itself a powerful tool for the many small bioinformatic tasks that you will encounter during everyday work. This module expects that you have done the steps in the Basic Unix module, i. e. it expects that you have already created certain folders and have copied the example data into your account. There are still small (hopefully not large) bugs lurking in this protocol. Please help improve it by adding comments.

Before you start

Log into your iceberg account and change to the directory NGS_workshop, that you created in the Basic Unix module:

cd NGS_workshop/Unix_module

I have downloaded my illumina read data. Now I want to know how many reads my sequence run has yielded.

zless sequence.fastq.gz
zcat sequence.fastq.gz | wc -l
man wc

Notes

Please feel free to post comments, questions, or improvements to this protocol. Happy to have your input!

1. List troubleshooting tips here.
2. You can also link to FAQs/tips provided by other sources such as the manufacturer or other websites.
3. Anecdotal observations that might be of use to others can also be posted here.

Please sign your name to your note by adding '''*~~~~''': to the beginning of your tip.

References

Relevant papers and books

1. Goldbeter, A and Koshland, DE (1981) - Proc Natl Acad Sci U S A 78(11) 6840-4 PMID 6947258
2. Jacob, F and Monod, J J (1961) - Mol Biol 3(3) 318-56 PMID 13718526
3. Ptashne, M (2004) Genetic Switch: Phage Lambda Revisited - Cold Spring Harbor Laboratory Press ISBN 0879697164

Contact

• Who has experience with this protocol?

or instead, discuss this protocol.