lecture-4 - Practical Bioinformatics for Life Scientists...

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Practical Bioinformatics for Life Scientists Week 2, Lecture 4 István Albert Bioinformatics Consulting Center Penn State
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Shell scripts Collect multiple commands into a single program This allows you to the same commands at another time or other data Document the steps and describe the thought process
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The shell is a programming environment Execute it with: sh commands.sh (there are other ways to execute shell scripts)
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Make your script more informative
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Running the shell script From now on print out your scripts for the homework whenever possible. Add the description into the script as comments that is the best place to keep it. This is not entirely correct, the quality string may also have the motif in it although with far less chance.
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Bash has lots of features We will slowly introduce some features along the way
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Fastx toolkit Install it by the instructions sent out via the email.
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Fasta/Fastq toolset Tip auto-completion: type a small part of the name fast then quickly press TAB twice
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Get help with the h flag
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Generate a quality plot Generated with fastx Generated with fastqc undocumented feature
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after filtering before filtering
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This note was uploaded on 02/29/2012 for the course BMMB 597D taught by Professor Istvanalbert during the Fall '11 term at Pennsylvania State University, University Park.

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lecture-4 - Practical Bioinformatics for Life Scientists...

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