Chris:LabNotes/Microbiome/2013/2013-5-15: Difference between revisions
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**<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) | **<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 | **<1c_Illumina_Test_Assembly_all-correction>: Assembly using only corrected reads for both 200bp and 2kb mate-paired read files | ||
*The steps for correction: (specifically for 1a_Illumina_Test_Assembly_Control) | |||
1) Make config files for pregraph, map, and GapCorrect | |||
*Pregraph config files <test_assembly_control.cfg> | |||
**Used parameters similar to Assemblathon2 | |||
**Key feature is that for both libraries, we are specifying the original read files (q1,q2) instead of the paired corrected file | |||
#maximal read length | |||
max_rd_len=200 | |||
[LIB] | |||
name=HB_gDNA200b_121224L1-4_filtered | |||
#average insert size | |||
avg_ins=200 | |||
#if sequence needs to be reversed | |||
reverse_seq=0 | |||
#in which part(s) the reads are used | |||
asm_flags=3 | |||
#in which order the reads are used while scaffolding | |||
rank=1 | |||
# cutoff of pair number for a reliable connection (default 3) | |||
pair_num_cutoff=3 | |||
q1=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA200b_121224L1-4_R1_filtered.fastq.gz | |||
q2=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA200b_121224L1-4_R2_filtered.fastq.gz | |||
[LIB] | |||
name=HB_gDNA2kb_NoIndex_L005_001_filtered | |||
avg_ins=2000 | |||
reverse_seq=1 | |||
asm_flags=2 | |||
rank=2 | |||
pair_num_cutoff=5 | |||
map_len=35 | |||
q1=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA2kb_NoIndex_L005_R1_001_filtered.fastq.gz | |||
q2=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA2kb_NoIndex_L005_R2_001_filtered.fastq.gz |
Revision as of 20:13, 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
- The steps for correction: (specifically for 1a_Illumina_Test_Assembly_Control)
1) Make config files for pregraph, map, and GapCorrect
- Pregraph config files <test_assembly_control.cfg>
- Used parameters similar to Assemblathon2
- Key feature is that for both libraries, we are specifying the original read files (q1,q2) instead of the paired corrected file
#maximal read length max_rd_len=200 [LIB] name=HB_gDNA200b_121224L1-4_filtered #average insert size avg_ins=200 #if sequence needs to be reversed reverse_seq=0 #in which part(s) the reads are used asm_flags=3 #in which order the reads are used while scaffolding rank=1 # cutoff of pair number for a reliable connection (default 3) pair_num_cutoff=3 q1=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA200b_121224L1-4_R1_filtered.fastq.gz q2=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA200b_121224L1-4_R2_filtered.fastq.gz [LIB] name=HB_gDNA2kb_NoIndex_L005_001_filtered avg_ins=2000 reverse_seq=1 asm_flags=2 rank=2 pair_num_cutoff=5 map_len=35 q1=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA2kb_NoIndex_L005_R1_001_filtered.fastq.gz q2=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA2kb_NoIndex_L005_R2_001_filtered.fastq.gz