Chris:LabNotes/Microbiome/2013/2013-5-15: Difference between revisions
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*The steps for correction: (specifically for 1a_Illumina_Test_Assembly_Control) | *The steps for correction: (specifically for 1a_Illumina_Test_Assembly_Control) | ||
1) Make config files for pregraph, map, and GapCorrect | 1) Make config files for pregraph, map, and GapCorrect | ||
*Pregraph config | *Pregraph config file <test_assembly_control.cfg> | ||
**Used parameters similar to Assemblathon2 | **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 | **Key feature is that for both libraries, we are specifying the original read files (q1,q2) instead of the paired corrected file | ||
Line 39: | Line 39: | ||
q1=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA2kb_NoIndex_L005_R1_001_filtered.fastq.gz | 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 | q2=/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA2kb_NoIndex_L005_R2_001_filtered.fastq.gz | ||
*Map config file <test_assembly_control.map.cfg> | |||
**Same as the pregraph config file, just without the max read length parameter | |||
[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 | |||
*Gap Closer config file <test_assembly_control.GC.cfg> | |||
**Only need to include library for 200bp reads (no need for scaffolding reads) | |||
[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 | |||
2) Write commands for assembly (ass.sh) | |||
*Here, we are writing commands for assembly in separate command lines (in order to better control each part of assembly) | |||
**Need commands for pregraph, contig, map, and scaff | |||
/home/cjwei/software/SOAPdenovo2-src-r223/standardPregraph/SOAPdenovo-63mer pregraph -s /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control.cfg -d 1 -p 32 -K 29 -o /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/pregraph.log | |||
/home/cjwei/software/SOAPdenovo2-src-r223/standardPregraph/SOAPdenovo-63mer contig -g /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control -M 3 >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/contig.log | |||
/home/cjwei/software/SOAPdenovo2-src-r223/standardPregraph/SOAPdenovo-63mer map -s /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control.map.cfg -g /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control -p 32 >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/map.log | |||
/home/cjwei/software/SOAPdenovo2-src-r223/standardPregraph/SOAPdenovo-63mer scaff -g /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control -b 1.2 -F -p 32 > /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/scaff.log | |||
3) Write command for GapCloser <GapCloser.sh> | |||
*This is performed after assembly and scaffolding | |||
/home/cjwei/software/SOAPdenovo2-src-r223/tools/GapCloser -a /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control.scafSeq -b /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control.GC.cfg -l 200 -o /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control.scafSeq.GC -p 29 -t 32 >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/GapCloser.log | |||
4) Create 1a_control_assembly in order to submit for Triton to run | |||
*'''The steps for assembly for using corrected 200bp and/or corrected 2kb reads were modified to switch q1,q2 to p in the config files in order to switch to corrected files''' |
Latest revision as of 20:29, 15 May 2013
Moleculo Data Analysis Part 2[edit]
- Continued from <http://genome-tech.ucsd.edu/LabNotes/index.php/Chris:LabNotes/Microbiome/2013/2013-5-14#Procedure>
1a-c_Illumina_Test_Assembly[edit]
- 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 file <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
- Map config file <test_assembly_control.map.cfg>
- Same as the pregraph config file, just without the max read length parameter
[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
- Gap Closer config file <test_assembly_control.GC.cfg>
- Only need to include library for 200bp reads (no need for scaffolding reads)
[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
2) Write commands for assembly (ass.sh)
- Here, we are writing commands for assembly in separate command lines (in order to better control each part of assembly)
- Need commands for pregraph, contig, map, and scaff
/home/cjwei/software/SOAPdenovo2-src-r223/standardPregraph/SOAPdenovo-63mer pregraph -s /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control.cfg -d 1 -p 32 -K 29 -o /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/pregraph.log
/home/cjwei/software/SOAPdenovo2-src-r223/standardPregraph/SOAPdenovo-63mer contig -g /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control -M 3 >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/contig.log
/home/cjwei/software/SOAPdenovo2-src-r223/standardPregraph/SOAPdenovo-63mer map -s /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control.map.cfg -g /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control -p 32 >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/map.log
/home/cjwei/software/SOAPdenovo2-src-r223/standardPregraph/SOAPdenovo-63mer scaff -g /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control -b 1.2 -F -p 32 > /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/scaff.log
3) Write command for GapCloser <GapCloser.sh>
- This is performed after assembly and scaffolding
/home/cjwei/software/SOAPdenovo2-src-r223/tools/GapCloser -a /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control.scafSeq -b /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control.GC.cfg -l 200 -o /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/test_assembly_control.scafSeq.GC -p 29 -t 32 >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1a_Illumina_Test_Assembly_Control/GapCloser.log
4) Create 1a_control_assembly in order to submit for Triton to run
- The steps for assembly for using corrected 200bp and/or corrected 2kb reads were modified to switch q1,q2 to p in the config files in order to switch to corrected files