Chris:LabNotes/Microbiome/2013/2013-5-15

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Revision as of 20:13, 15 May 2013 by >Cjwei
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Moleculo Data Analysis Part 2

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