Unix Tips and Tricks - Part 1
January 29, 2008
Exercises

Perform the following tasks and answer the questions.
Everything can be done with a Unix command or commands.

These exercises are at
	http://iona.wi.mit.edu/bio/education/hot_topics/unix1/unix_tips_tricks_1_ex.txt
Solutions are at
	http://iona.wi.mit.edu/bio/education/hot_topics/unix1/solutions_1.txt


0 - Open a Unix terminal on your computer

1 - Make a directory called "unix1" and enter it.

2 - Download the file - refSeq_hg18.zip from http://iona.wi.mit.edu/bio/education/hot_topics/unix1/refSeq_hg18.zip
	wget http://iona.wi.mit.edu/bio/education/hot_topics/unix1/refSeq_hg18.zip
	
3 - Unzip it: 
	unzip refSeq_hg18.zip
	
4 - Take a look at the file.  
	How many fields wide is it?
	How many lines long is it?

5 - The file shows human genome coordinates (March 2006 assembly) for all RefSeq transcripts.
	The fields are:
	1 - gene symbol
	2 - transcript ID/accession (NM_*)
	3 - chromosome
	4 - strand on reference chromosome
	5 - transcript "start" (really just one end of the transcript; the end for transcripts on the "-" chromosome)
	6 - transcript "end" (really just one end of the transcript; the start for transcripts on the "-" chromosome)
	Introns may be included, so be aware that not all intervening sequence is necessarily transcribed sequence.
	
6 - What are the fields delimited by?

7 - How many transcripts (NM_*) are represented in the file?

8 - How many genes are represented in the file?

9 - Are any transcripts represented more than once?  Why might this be?  
    If so, which [Put the list in the file "mult_transcripts.txt"]?

10- How many chromosomes are represented?

11- What genes are on chromosome Y?  Put these in the file "chrY_genes.txt"

12- Sort all the data, first by chromosome (ascending) and then by the first coordinate (descending).

13- Make separate files for the "+" and "-" strand genes, called "refSeq_hg18_plus.txt" and "refSeq_hg18_neg.txt"

14- Split all the data about evenly into 4 files called "Part_1.txt", "Part_2.txt", etc.

15- What 5 genes appear on the "right end" (e.g., have the highest coordinates) of chr 19?

16- Based upon regions with genes, what's the longest chromosome?  At least how long is it?

17- What genes contain the letters "BMP"?  Put them in the file "BMPs_etc.txt"

18- Which of these "BMP genes" have more than one transcript?

19- What gene has the longest genomic length (distance between transcript start and end)?  The shortest?

20- Reformat the file so it has two fields like this:  RefSeq<tab>chr:start-end
	ex: NM_001039886	chr19:57722720-57751115

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