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assignments:ex8 [2018/10/04 08:31]
dokuroot
assignments:ex8 [2018/10/04 09:04] (current)
dokuroot
Line 33: Line 33:
   $ velveth velvet_output 35 -fastq -shortPaired -separate fastq_file1.fastq fastq_file1.fastq   $ velveth velvet_output 35 -fastq -shortPaired -separate fastq_file1.fastq fastq_file1.fastq
 **10.** Use ''​velvetg''​ to assemble the reads into contigs and build a graph. Specify an expected coverage of 21 (determined prior to this exercise based on the size of the E. coli genome and the number and length of reads). Selecting '​-read_trkg yes' and '​-amos_file yes' options will generate a file with contig information that can be viewed with the graphical viewing software '​Tablet'​. **10.** Use ''​velvetg''​ to assemble the reads into contigs and build a graph. Specify an expected coverage of 21 (determined prior to this exercise based on the size of the E. coli genome and the number and length of reads). Selecting '​-read_trkg yes' and '​-amos_file yes' options will generate a file with contig information that can be viewed with the graphical viewing software '​Tablet'​.
-  $  velvetg velvet_output ​-exp_cov 21 -read_trkg yes -amos_file yes+  $  velvetg velvet_output -read_trkg yes -amos_file yes
 **11.** In the terminal, change into '​velvet_output'​ directory using ''​cd''​. Examine the '​contigs.fa'​ files using ''​more''​. This file contains all of the assembled contigs.\\ \\ **11.** In the terminal, change into '​velvet_output'​ directory using ''​cd''​. Examine the '​contigs.fa'​ files using ''​more''​. This file contains all of the assembled contigs.\\ \\
 **12.** Plot the data in '​Tablet'​ using ''​open velvet_asm.afg''​ or by double clicking the file. Examine some of the contigs. How many contigs were produced and what was the size range and average size? Record this information in your lab notebook. **12.** Plot the data in '​Tablet'​ using ''​open velvet_asm.afg''​ or by double clicking the file. Examine some of the contigs. How many contigs were produced and what was the size range and average size? Record this information in your lab notebook.
assignments/ex8.txt ยท Last modified: 2018/10/04 09:04 by dokuroot