# NSCI 580A3 fall 2017

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wiki:2016assignment2

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 wiki:2016assignment2 [2016/08/31 16:08]erin wiki:2016assignment2 [2016/08/31 16:09] (current)erin Both sides previous revision Previous revision 2016/08/31 16:09 erin 2016/08/31 16:08 erin 2016/08/31 16:07 erin 2016/08/31 16:03 erin 2016/08/31 15:59 erin 2016/08/31 15:57 erin 2016/08/31 15:56 erin 2016/08/31 15:56 erin 2016/08/31 15:40 erin 2016/08/31 15:36 erin 2016/08/31 15:35 erin 2016/08/31 15:34 erin 2016/08/30 15:23 erin 2016/08/30 12:33 erin 2016/08/30 12:31 erin created 2016/08/31 16:09 erin 2016/08/31 16:08 erin 2016/08/31 16:07 erin 2016/08/31 16:03 erin 2016/08/31 15:59 erin 2016/08/31 15:57 erin 2016/08/31 15:56 erin 2016/08/31 15:56 erin 2016/08/31 15:40 erin 2016/08/31 15:36 erin 2016/08/31 15:35 erin 2016/08/31 15:34 erin 2016/08/30 15:23 erin 2016/08/30 12:33 erin 2016/08/30 12:31 erin created Line 28: Line 28: $grep '​^apple'​ file.txt$grep '​^apple'​ file.txt ​ This would find only instances of the word ''​apple''​ that appeared at the beginning of a line. See how you could use ''​^''​ to pull out just the tab-delimited portion of the .gff file and save it as ''​sacCer3_tdt_annotation.gff''​. What command did you use? ​ This would find only instances of the word ''​apple''​ that appeared at the beginning of a line. See how you could use ''​^''​ to pull out just the tab-delimited portion of the .gff file and save it as ''​sacCer3_tdt_annotation.gff''​. What command did you use? - - Say we want to start with the file ''​sacCer3_tdt_annotation.gff''​ and extract out annotation lines for ONLY the nuclear-encoded tRNAs. What piped series of commands would you use to (1) extract out just the lines that contain '​tRNA'​ entries (in the third column), (2) remove any lines that contain '​chrMito',​ and (3) save the resulting file with the name ''​sacCer3_tRNA_minusMito.gff''​ (hint1: ​you'll use a grep command, another grep command, and a redirection. hint2: You may need to get tricky to extract the '​tRNA'​ entries. Think '​\t'​. + - Say we want to start with the file ''​sacCer3_tdt_annotation.gff''​ and extract out annotation lines for ONLY the nuclear-encoded tRNAs. What piped series of commands would you use to (1) extract out just the lines that contain '​tRNA'​ entries (in the third column), (2) remove any lines that contain '​chrMito',​ and (3) save the resulting file with the name ''​sacCer3_tRNA_minusMito.gff''​ (hint1: ​I used a grep command, another grep command, and a redirection. hint2: You may need to get tricky to extract the '​tRNA'​ entries. Think '​\t'​. - How many lines are in your ''​sacCer3_tRNA_minusMito.gff''​ file? - How many lines are in your ''​sacCer3_tRNA_minusMito.gff''​ file? - - Write a series of piped commands that will allow you to test that '​tRNA'​ is the only uniq entry in the 3rd column of ''​sacCer3_tRNA_minusMito.gff''​ file. What are they? + - Write a series of piped commands that will allow you to test that '​tRNA'​ is the only unique ​entry in the 3rd column of ''​sacCer3_tRNA_minusMito.gff''​ file. What are they? - A .bed file is a standardized file type that contains four columns of information:​ (1) chromosome name, (2) start, (3) stop, (3) strand. Can you execute a code that will convert your ''​sacCer3_tRNA_minusMito.gff''​ file into a bed file? Save it as ''​sacCer3_tRNA.bed''​. (hint: see the ''​cut''​ man pages and look at the examples) - A .bed file is a standardized file type that contains four columns of information:​ (1) chromosome name, (2) start, (3) stop, (3) strand. Can you execute a code that will convert your ''​sacCer3_tRNA_minusMito.gff''​ file into a bed file? Save it as ''​sacCer3_tRNA.bed''​. (hint: see the ''​cut''​ man pages and look at the examples) - Let's say you want to make a custom command that converts gff files into bed files. How would you make a command called ''​gff2bed''​ using alias? - Let's say you want to make a custom command that converts gff files into bed files. How would you make a command called ''​gff2bed''​ using alias? - - -