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2_Transcriptome assembly
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2_Transcriptome assembly
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-------------------------------------------------------------------------------------------------------
#Compiled assembly
Trinity --output tuco_compiled_trinity --full_cleanup --seqType fq --max_memory 60G --CPU 16 --trimmomatic \
--quality_trimming_params "ILLUMINACLIP:/data/andrew/adapters/TruSeq3-PE.fa:2:40:15 LEADING:2 TRAILING:2 MINLEN:25" \
--left /data/andrew/reads_corrected/tuco_hippocampus.1.cor.fq,/data/andrew/reads_corrected/tuco_hypothalamus.1.cor.fq,/data/andrew/reads_corrected/tuco_kidney.1.cor.fq,/data/andrew/reads_corrected/tuco_liver.1.cor.fq,/data/andrew/reads_corrected/tuco_ovary.1.cor.fq,/data/andrew/reads_corrected/tuco_skin.1.cor.fq,/data/andrew/reads_corrected/tuco_spleen.1.cor.fq,/data/andrew/reads_corrected/tuco_testes.1.cor.fq \
--right /data/andrew/reads_corrected/tuco_hippocampus.2.cor.fq,/data/andrew/reads_corrected/tuco_hypothalamus.2.cor.fq,/data/andrew/reads_corrected/tuco_kidney.2.cor.fq,/data/andrew/reads_corrected/tuco_liver.2.cor.fq,/data/andrew/reads_corrected/tuco_ovary.2.cor.fq,/data/andrew/reads_corrected/tuco_skin.2.cor.fq,/data/andrew/reads_corrected/tuco_spleen.2.cor.fq,/data/andrew/reads_corrected/tuco_testes.2.cor.fq
-------------------------------------------------------------------------------------------------------
#Individual Tissue transcriptome assembly
Trinity --output tuco_hippocampus.assembly.trinity --full_cleanup --seqType fq --max_memory 60G --CPU 25 --trimmomatic \
--quality_trimming_params "ILLUMINACLIP:/data/andrew/adapters/TruSeq3-PE.fa:2:40:15 LEADING:2 TRAILING:2 MINLEN:25" \
--left /data/andrew/reads_corrected/tuco_hippocampus.1.cor.fq \
--right /data/andrew/reads_corrected/tuco_hippocampus.2.cor.fq
Trinity --output tuco_hypothalamus.assembly.trinity --full_cleanup --seqType fq --max_memory 60G --CPU 25 --trimmomatic \
--quality_trimming_params "ILLUMINACLIP:/data/andrew/adapters/TruSeq3-PE.fa:2:40:15 LEADING:2 TRAILING:2 MINLEN:25" \
--left /data/andrew/reads_corrected/tuco_hypothalamus.1.cor.fq \
--right /data/andrew/reads_corrected/tuco_hypothalamus.2.cor.fq
Trinity --output tuco_kidney.assembly.trinity --full_cleanup --seqType fq --max_memory 60G --CPU 25 --trimmomatic \
--quality_trimming_params "ILLUMINACLIP:/data/andrew/adapters/TruSeq3-PE.fa:2:40:15 LEADING:2 TRAILING:2 MINLEN:25" \
--left /data/andrew/reads_corrected/tuco_kidney.1.cor.fq \
--right /data/andrew/reads_corrected/tuco_kidney.2.cor.fq
Trinity --output tuco_liver.assembly.trinity --full_cleanup --seqType fq --max_memory 60G --CPU 25 --trimmomatic \
--quality_trimming_params "ILLUMINACLIP:/data/andrew/adapters/TruSeq3-PE.fa:2:40:15 LEADING:2 TRAILING:2 MINLEN:25" \
--left /data/andrew/reads_corrected/tuco_liver.1.cor.fq \
--right /data/andrew/reads_corrected/tuco_liver.2.cor.fq
Trinity --output tuco_ovary.assembly.trinity --full_cleanup --seqType fq --max_memory 60G --CPU 25 --trimmomatic \
--quality_trimming_params "ILLUMINACLIP:/data/andrew/adapters/TruSeq3-PE.fa:2:40:15 LEADING:2 TRAILING:2 MINLEN:25" \
--left /data/andrew/reads_corrected/tuco_ovary.1.cor.fq \
--right /data/andrew/reads_corrected/tuco_ovary.2.cor.fq
Trinity --output tuco_skin.assembly.trinity --full_cleanup --seqType fq --max_memory 60G --CPU 25 --trimmomatic \
--quality_trimming_params "ILLUMINACLIP:/data/andrew/adapters/TruSeq3-PE.fa:2:40:15 LEADING:2 TRAILING:2 MINLEN:25" \
--left /data/andrew/reads_corrected/tuco_skin.1.cor.fq \
--right /data/andrew/reads_corrected/tuco_skin.2.cor.fq
Trinity --output tuco_spleen.assembly.trinity --full_cleanup --seqType fq --max_memory 60G --CPU 25 --trimmomatic \
--quality_trimming_params "ILLUMINACLIP:/data/andrew/adapters/TruSeq3-PE.fa:2:40:15 LEADING:2 TRAILING:2 MINLEN:25" \
--left /data/andrew/reads_corrected/tuco_spleen.1.cor.fq \
--right /data/andrew/reads_corrected/tuco_spleen.2.cor.fq
Trinity --output tuco_testes.assembly.trinity --full_cleanup --seqType fq --max_memory 60G --CPU 25 --trimmomatic \
--quality_trimming_params "ILLUMINACLIP:/data/andrew/adapters/TruSeq3-PE.fa:2:40:15 LEADING:2 TRAILING:2 MINLEN:25" \
--left /data/andrew/reads_corrected/tuco_testes.1.cor.fq \
--right /data/andrew/reads_corrected/tuco_testes.2.cor.fq
-------------------------------------------------------------------------------------------------------
#Individual Tissue transcriptome assembly with normalization of 100x
Trinity --output tuco_hippocampus.norm_trinity --full_cleanup --seqType fq --max_memory 60G --CPU 20 --normalize_max_read_cov 100 --trimmomatic \
--quality_trimming_params "ILLUMINACLIP:/data/andrew/adapters/TruSeq3-PE.fa:2:40:15 LEADING:2 TRAILING:2 MINLEN:25" \
--left /data/andrew/reads_corrected/tuco_hippocampus.1.cor.fq \
--right /data/andrew/reads_corrected/tuco_hippocampus.2.cor.fq
Trinity --output tuco_hypothalamus.norm_trinity --full_cleanup --seqType fq --max_memory 60G --CPU 20 --normalize_max_read_cov 100 --trimmomatic \
--quality_trimming_params "ILLUMINACLIP:/data/andrew/adapters/TruSeq3-PE.fa:2:40:15 LEADING:2 TRAILING:2 MINLEN:25" \
--left /data/andrew/reads_corrected/tuco_hypothalamus.1.cor.fq \
--right /data/andrew/reads_corrected/tuco_hypothalamus.2.cor.fq
Trinity --output tuco_kidney.norm_trinity --full_cleanup --seqType fq --max_memory 60G --CPU 20 --normalize_max_read_cov 100 --trimmomatic \
--quality_trimming_params "ILLUMINACLIP:/data/andrew/adapters/TruSeq3-PE.fa:2:40:15 LEADING:2 TRAILING:2 MINLEN:25" \
--left /data/andrew/reads_corrected/tuco_kidney.1.cor.fq \
--right /data/andrew/reads_corrected/tuco_kidney.2.cor.fq
Trinity --output tuco_liver.norm_trinity --full_cleanup --seqType fq --max_memory 60G --CPU 20 --normalize_max_read_cov 100 --trimmomatic \
--quality_trimming_params "ILLUMINACLIP:/data/andrew/adapters/TruSeq3-PE.fa:2:40:15 LEADING:2 TRAILING:2 MINLEN:25" \
--left /data/andrew/reads_corrected/tuco_liver.1.cor.fq \
--right /data/andrew/reads_corrected/tuco_liver.2.cor.fq
Trinity --output tuco_ovary.norm_trinity --full_cleanup --seqType fq --max_memory 60G --CPU 20 --normalize_max_read_cov 100 --trimmomatic \
--quality_trimming_params "ILLUMINACLIP:/data/andrew/adapters/TruSeq3-PE.fa:2:40:15 LEADING:2 TRAILING:2 MINLEN:25" \
--left /data/andrew/reads_corrected/tuco_ovary.1.cor.fq \
--right /data/andrew/reads_corrected/tuco_ovary.2.cor.fq
Trinity --output tuco_skin.norm_trinity --full_cleanup --seqType fq --max_memory 60G --CPU 20 --normalize_max_read_cov 100 --trimmomatic \
--quality_trimming_params "ILLUMINACLIP:/data/andrew/adapters/TruSeq3-PE.fa:2:40:15 LEADING:2 TRAILING:2 MINLEN:25" \
--left /data/andrew/reads_corrected/tuco_skin.1.cor.fq \
--right /data/andrew/reads_corrected/tuco_skin.2.cor.fq
Trinity --output tuco_spleen.norm_trinity --full_cleanup --seqType fq --max_memory 60G --CPU 20 --normalize_max_read_cov 100 --trimmomatic \
--quality_trimming_params "ILLUMINACLIP:/data/andrew/adapters/TruSeq3-PE.fa:2:40:15 LEADING:2 TRAILING:2 MINLEN:25" \
--left /data/andrew/reads_corrected/tuco_spleen.1.cor.fq \
--right /data/andrew/reads_corrected/tuco_spleen.2.cor.fq
Trinity --output tuco_testes.norm_trinity --full_cleanup --seqType fq --max_memory 60G --CPU 20 --normalize_max_read_cov 100 --trimmomatic \
--quality_trimming_params "ILLUMINACLIP:/data/andrew/adapters/TruSeq3-PE.fa:2:40:15 LEADING:2 TRAILING:2 MINLEN:25" \
--left /data/andrew/reads_corrected/tuco_testes.1.cor.fq \
--right /data/andrew/reads_corrected/tuco_testes.2.cor.fq