Chris:LabNotes/Microbiome/2013/2013-5-14: Difference between revisions

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**correct_error
**correct_error
*Steps for error correction:
*Steps for error correction:
0) Need to gzip read files prior to error correction (can also use .gz files for assembly in SOAPdenovo)
1)Create read list for correction <reads2cor.lst>, which is just the file location of reads.  If have paired read files, must put each file consecutively.
1)Create read list for correction <reads2cor.lst>, which is just the file location of reads.  If have paired read files, must put each file consecutively.
  /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA200b_121224L1-4_R1_filtered.fastq.gz
  /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA200b_121224L1-4_R1_filtered.fastq.gz
Line 30: Line 32:
  /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA2kb_NoIndex_L005_R1_001_filtered.fastq.gz
  /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA2kb_NoIndex_L005_R1_001_filtered.fastq.gz
  /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA2kb_NoIndex_L005_R2_001_filtered.fastq.gz
  /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA2kb_NoIndex_L005_R2_001_filtered.fastq.gz
2) Run commands (need to run kmerfreq then correct_error scripts in order) <1_correction>
2) Run commands (need to run kmerfreq then correct_error scripts in order) <1_correction>
/home/cjwei/software/SOAPdenovo2-src-r223/SOAPdenovoPipeline4BirdInAssemblathon2/kmerfreq -k 27 -l /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1_Illumina_Test_Assembly/reads2cor.lst -p /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1_Illumina_Test_Assembly/test_assembly -t 32 -i 400000000 -L 200 >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1_Illumina_Test_Assembly/kmerfreq.log
/home/cjwei/software/SOAPdenovo2-src-r223/SOAPdenovoPipeline4BirdInAssemblathon2/correct_error -k 27 -l 2 -a 0 -e 1 -w 1 -q 35 -t 32 -j 1 /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1_Illumina_Test_Assembly/test_assembly.freq.gz /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1_Illumina_Test_Assembly/reads2cor.lst >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1_Illumina_Test_Assembly/correct.log
3) Output can be found in original raw read folder as .cor.pair files because program combines the paired read files into one </projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/>
HB_gDNA200b_121224L1-4_R1_filtered.fastq.gz.cor.pair
HB_gDNA2kb_NoIndex_L005_R1_001_filtered.fastq.gz.cor.pair

Revision as of 18:48, 15 May 2013

Moleculo Data Analysis Part 1

Background

  • We are integrating Illumina (short read) and Moleculo (long read) data to assemble the oncomelania genome
  • The overall plan that we are using is:
Test assembly of small Illumina dataset
         |
         V
Validation of assembly (using assembly statistics and core genes search)
         |
         V
Assembly of whole Illumina dataset
         |
         V
Integration of Moleculo with Illumina reads
         |
         V
Validation of hybrid assembly (assembly statistics, core genes search, assembly errors)

Procedure

0_Illumina_Test_correction

  • Triton Folder: </projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/0_Illumina_Test_correction/>
  • In order to first start with the test assembly of small Illumina dataset, we first want to perform correction of reads and test whether correction will help improve assembly
  • We are using the correction software used in Assemblathon2 by SOAPdenovo: (found in </home/cjwei/software/SOAPdenovo2-src-r223/SOAPdenovoPipeline4BirdInAssemblathon2/>
    • kmerfreq
    • correct_error
  • Steps for error correction:

0) Need to gzip read files prior to error correction (can also use .gz files for assembly in SOAPdenovo)

1)Create read list for correction <reads2cor.lst>, which is just the file location of reads. If have paired read files, must put each file consecutively.

/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA200b_121224L1-4_R1_filtered.fastq.gz
/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA200b_121224L1-4_R2_filtered.fastq.gz
/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA2kb_NoIndex_L005_R1_001_filtered.fastq.gz
/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/HB_gDNA2kb_NoIndex_L005_R2_001_filtered.fastq.gz

2) Run commands (need to run kmerfreq then correct_error scripts in order) <1_correction>

/home/cjwei/software/SOAPdenovo2-src-r223/SOAPdenovoPipeline4BirdInAssemblathon2/kmerfreq -k 27 -l /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1_Illumina_Test_Assembly/reads2cor.lst -p /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1_Illumina_Test_Assembly/test_assembly -t 32 -i 400000000 -L 200 >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1_Illumina_Test_Assembly/kmerfreq.log 
/home/cjwei/software/SOAPdenovo2-src-r223/SOAPdenovoPipeline4BirdInAssemblathon2/correct_error -k 27 -l 2 -a 0 -e 1 -w 1 -q 35 -t 32 -j 1 /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1_Illumina_Test_Assembly/test_assembly.freq.gz /projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1_Illumina_Test_Assembly/reads2cor.lst >/projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Hybrid_Assembly_5_14_2013/1_Illumina_Test_Assembly/correct.log

3) Output can be found in original raw read folder as .cor.pair files because program combines the paired read files into one </projects/zhang-lab/cjwei/130419_Oncomelania_Ilumina_Moleculo/Illumina_raw/>

HB_gDNA200b_121224L1-4_R1_filtered.fastq.gz.cor.pair
HB_gDNA2kb_NoIndex_L005_R1_001_filtered.fastq.gz.cor.pair