# NSCI 580A3 fall 2017

### Site Tools

assignments:assignment3

# Differences

This shows you the differences between two versions of the page.

 assignments:assignment3 [2016/09/07 16:18]tai assignments:assignment3 [2016/09/07 16:20] (current)tai Both sides previous revision Previous revision 2016/09/07 16:20 tai 2016/09/07 16:18 tai 2016/09/07 16:17 tai 2016/09/07 16:16 tai 2016/09/07 16:13 tai 2016/09/06 13:05 tai 2016/09/05 18:34 tai 2016/09/02 16:06 tai 2016/09/02 16:05 tai 2016/08/31 12:30 tai 2016/08/29 14:04 tai 2016/08/29 12:57 tai 2016/08/02 14:47 external edit2015/12/10 09:16 asa 2015/12/08 17:30 asa 2015/12/08 12:50 asa 2015/12/06 10:35 asa 2015/12/04 15:40 asa 2015/12/04 15:40 asa 2015/12/04 15:36 asa 2015/12/04 15:29 asa 2015/12/04 15:29 asa 2015/12/04 15:27 asa 2015/12/04 10:43 asa 2015/12/04 10:43 asa 2015/10/15 12:24 asa 2015/10/09 13:11 asa 2016/09/07 16:20 tai 2016/09/07 16:18 tai 2016/09/07 16:17 tai 2016/09/07 16:16 tai 2016/09/07 16:13 tai 2016/09/06 13:05 tai 2016/09/05 18:34 tai 2016/09/02 16:06 tai 2016/09/02 16:05 tai 2016/08/31 12:30 tai 2016/08/29 14:04 tai 2016/08/29 12:57 tai 2016/08/02 14:47 external edit2015/12/10 09:16 asa 2015/12/08 17:30 asa 2015/12/08 12:50 asa 2015/12/06 10:35 asa 2015/12/04 15:40 asa 2015/12/04 15:40 asa 2015/12/04 15:36 asa 2015/12/04 15:29 asa 2015/12/04 15:29 asa 2015/12/04 15:27 asa 2015/12/04 10:43 asa 2015/12/04 10:43 asa 2015/10/15 12:24 asa 2015/10/09 13:11 asa 2015/10/09 13:10 asa [Submission] 2015/10/07 12:04 asa 2015/10/02 12:42 asa 2015/10/02 12:12 asa 2015/10/02 12:12 asa 2015/10/02 12:10 asa 2015/10/02 12:08 asa [Submission] 2015/10/02 12:05 asa 2015/10/02 10:04 asa 2015/10/02 09:48 asa 2015/10/02 09:42 asa 2013/10/09 20:38 asa [Part 4: Using SVMs] 2013/10/09 12:19 asa 2013/10/06 20:54 asa 2013/10/06 20:51 asa 2013/10/06 15:23 asa 2013/10/06 15:23 asa 2013/10/06 15:22 asa 2013/10/06 13:33 asa 2013/10/06 11:54 asa 2013/10/06 11:54 asa 2013/10/06 11:52 asa 2013/10/04 21:08 asa [Part 3: Using the SVM] 2013/10/04 21:06 asa Line 52: Line 52: 7. Extract just the line of the file that contains the alg-1 "​gene"​ coordinates using **grep** (you will actually get two lines that have the gene coordinates). ​ //What information can be used to distinguish just the genomic coordinates from other features such that you extract only one line of information?//​ \\ \\ 7. Extract just the line of the file that contains the alg-1 "​gene"​ coordinates using **grep** (you will actually get two lines that have the gene coordinates). ​ //What information can be used to distinguish just the genomic coordinates from other features such that you extract only one line of information?//​ \\ \\ 8. Repeat steps 4-7 on the compressed file using compressed file friendly commands. \\ \\ 8. Repeat steps 4-7 on the compressed file using compressed file friendly commands. \\ \\ - 9. Extract the lines containing the genomic ​coordinates ​of all genes into a new file using **grep**. ​ //How many lines are in your new file?  How many genes do you think C. elegans contains and is the number of lines you extracted consistent with what you would predict? It is likely that there are far more lines than the number of genes you would expect because each gene may have multiple entries. Next week, we'll discuss how to further restrict the search using regular expressions.//​ \\ \\ + 9. Extract the lines containing the "​gene" ​coordinates ​for all genes into a new file using **grep**. ​ //How many lines are in your new file?  How many genes do you think C. elegans contains and is the number of lines you extracted consistent with what you would predict? It is likely that there are far more lines than the number of genes you would expect because each gene may have multiple entries. Next week, we'll discuss how to further restrict the search using regular expressions.//​ \\ \\ 10. On the original compressed table, extract the lines of the file containing the genomic coordinates of all exons into a new file (any lines that contain the word exon). //How many lines are in your new file?  How many exons do you think each C. elegans gene has on average and is the number of lines you extracted consistent with what you would predict?// \\ \\ 10. On the original compressed table, extract the lines of the file containing the genomic coordinates of all exons into a new file (any lines that contain the word exon). //How many lines are in your new file?  How many exons do you think each C. elegans gene has on average and is the number of lines you extracted consistent with what you would predict?// \\ \\ 11. Transfer the file into your directory on the montgomery lab server. This will serve as confirmation that you completed the exercise. \\ \\ 11. Transfer the file into your directory on the montgomery lab server. This will serve as confirmation that you completed the exercise. \\ \\