Metatranscriptomics data analysis
This repository describes step by step the analysis of the Metatranscriptome dataset
A continuous effort to create a reliable pipeline for;
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Quality control
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Removing host RNAs
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Taxonomic assignment
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Denovo assembly
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Differential gene expression
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Functional annotation
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Pathway analysis
Quality control
fastp -q 5 -l 25 -3 -M 5 -i ${sampleid}_R1_001.fastq.gz -I ${sampleid}_R2_001.fastq.gz -o ./clean_data/${sampleid}_R1_001.clean_fastq.gz -O ./clean_data/${sampleid}_R2_001.clean_fastq.gz --html ./clean_data/fastqc_results/${sampleid}_fastq_trim_report.html
Removing host RNAs
bbsplit.sh in1=${sampleid}_R1_001.clean_fastq.gz in2=${sampleid}_R2_001.clean_fastq.gz ref=../refferences/coral.fna.gz basename=./contaminats_free/out_%.fq.gz outu1=./contaminats_free/${sampleid}_R1_001.contfree_fastq.gz outu2=./contaminats_free/${sampleid}_R2_001.contfree_fastq.gz
Taxonomic assignment
kraken2 --use-names --threads 20 --db ../databases/minikraken_8GB_20200312 --fastq-input --report ../kraken_results/mysample.kreport2 --gzip-compressed --paired ${sampleid}_R1_001.contfree_fastq.gz ${sampleid}_R2_001.contfree_fastq.gz > ../kraken_results/${sampleid}.krk
Taxonomy visualization
rcf -n /home/cley/recentrifuge/taxdump -k ${sampleid} -c 1 -o ../recentrifuge_results/${sampleid}.html
Denovo assembly
Trinity --seqType fq --max_memory 100G -βleft all_reads_R1.fa.fq β-right all_reads_R2.fa.fq --SS_lib_type RF --CPU 48 --output trinity_results
Differential expression
DE_Updated.Rmd
Functional annotation and pathways analysis
pathways_Plotting