Chris:LabNotes/Microbiome/2013/2013-5-15: Difference between revisions
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=== | =Moleculo Data Analysis Part 2= | ||
*Continued from <http://genome-tech.ucsd.edu/LabNotes/index.php/Chris:LabNotes/Microbiome/2013/2013-5-14#Procedure> | |||
===1a-c_Illumina_Test_Assembly=== | |||
*Triton folder: </projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/> | |||
*We are going to now run SOAPdenovo2 assembly on corrected read files | |||
*In order to do this, we are going to test three different conditions for assembly (each found in their consecutive folders): | |||
**<1a_Illumina_Test_Assembly_Control>: Assembly using only non-corrected original reads | |||
**<1b_Illumina_Test_Assembly_no-Mate-correction>: Assembly using corrected 200bp reads with no correction on mate-paired 2kb reads (this is the protocol used in Assemblathon2 in which the reads used to scaffold are not corrected) | |||
**<1c_Illumina_Test_Assembly_all-correction>: Assembly using only corrected reads for both 200bp and 2kb mate-paired read files |
Revision as of 19:07, 15 May 2013
Moleculo Data Analysis Part 2
- Continued from <http://genome-tech.ucsd.edu/LabNotes/index.php/Chris:LabNotes/Microbiome/2013/2013-5-14#Procedure>
1a-c_Illumina_Test_Assembly
- Triton folder: </projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/>
- We are going to now run SOAPdenovo2 assembly on corrected read files
- In order to do this, we are going to test three different conditions for assembly (each found in their consecutive folders):
- <1a_Illumina_Test_Assembly_Control>: Assembly using only non-corrected original reads
- <1b_Illumina_Test_Assembly_no-Mate-correction>: Assembly using corrected 200bp reads with no correction on mate-paired 2kb reads (this is the protocol used in Assemblathon2 in which the reads used to scaffold are not corrected)
- <1c_Illumina_Test_Assembly_all-correction>: Assembly using only corrected reads for both 200bp and 2kb mate-paired read files