Pulling out individual chromosomes from fasta file

This is probably only useful under certain instances, but I thought I would share.

Using sed, you can grab a single chromosome from a fasta file.

sed -n '/>chr1/,/>chr2/p' <fasta>

Note that you can use this to grab multiple consecutive chromosomes too.

sed -n '/>chr1/,/>chr4/p' <fasta>

Get the nth base from a certain chromosome in a fasta file

I was trying to write my own tool to do this, but I doubt I could make it run as fast or faster than an existing tool.

Turns out samtools does the trick.

http://seqanswers.com/forums/showthread.php?t=17315

samtools faidx <fasta.fa> <seq>:<pos>-<pos>

For example, to get the 6078th base in chr 3:
samtools faidx <fasta.fa> chr3:6078-6078

Grab random lines from a file with Unix

It is very easy to grab a random set of lines from a file using BASH.  There is a built in command called shuf that you can use.

For example,
To extract 1 random line from a file:
shuf -n 1 <file>

To extract 5 random lines from a file:
shuf -n 5 <file>

Pulling sections out of FastQC output file

This is fairly straightforward.  The output file generated by FastQC puts dividers in the data already.  They look like the following:
>>Basic Statistics
>>END_MODULE

This is useful for if we want to separate the data.  You can do so with the following script.

https://github.com/agduncan94/BioinformaticTools/blob/master/grabFastQCOutput.pl

I'm sure there are better ways, but if you just want to do it quickly then this will work.

Using tmux to split terminal windows

Before using tmux, it was very common that I had 5 or 6 terminal windows open (I don't like using tabs). This made it very hard to navigate between each window, especially since I only have two small screens.  Having other programs like Firefox open just added to the clutter.  With tmux I can lower the amount of windows to just 1 or 2, and that is done by splitting the windows.

I find having multiple panes in a window is very useful for having one dedicated to writing code, another for running code, and a third for processes.  You may find different combinations which work best for you.  Typically I have one pane no the top half and the bottom half is split into two panes side by side.

Tmux has a lot of features besides splitting windows, but this tutorial just looks at the splitting windows feature.

Useful commands
ctrl-b " - split horizontally
ctrl-b % - split vertically
ctrl-b x - close pane
ctrl-b <arrow key> - navigate between panes.

1. Split horizontally
ctrl-b "

2. Split vertically
ctrl-b %

3. Split into three
 ctrl-b "
To get a split row on the bottom, navigate to the bottom pane and do
ctrl-b %
The process is similar for if you want to split the top row.