Systematic Analysis for Quantification of Everything (SAQE) is a set of scripts for quantification of transcripts using RNA-seq and metagenomic results. SAQE consists of several scripts to do the analyses. The number added in the name of script corresponds to the analysis bewlo.
- Expression (original SAQE(Systematic Analysis for Quantification of Expression))
- 01 Retrieval of RNA-seq reads from the SRA database
- 02 Conversion of data format and compression
- 03 Trimming and quality control of reads
- 04 Transcriptome assembly by Trinity (skip if the transcriptome reference is available)
- 05 Expression quantification by salmon ((direct) salmon or align_and_estimate_abundance.pl (AAEA) with salmon)
- Functional annotation (Fanflow)
- 11 Translating cDNA into protein sequence
- 12 Getting reference protein sequences
- 13 Making BLAST index & Executing BLAST search (BLASTP)
- 15 Executing global alignment search by ggsearch and extract needed information for further studies
- 16 Getting Pfam and running HMMscan with parser for the functional annotation
- Metagenome: see
101Kraken2.mdfor details- 101 Building libarary Kraken2 for Kraken2
- 102 Running Kraken2 for classification
- 103 Visualizing multiple Kraken2 outputs for comparison
- Miniconda is required to install
sra-tools,trim-galoreandpigz. - Docker is also required to do the analyses in Trinity (04) and salmon (05).
- Pitagora Workflows in Common Workflow Language (CWL) at https://github.com/pitagora-network/pitagora-cwl is required to run salmon script (05).
Cite the paper below for the citation.
- For expression part:
Bono H. Meta-Analysis of Oxidative Transcriptomes in Insects. Antioxidants. 2021; 10(3):345.
https://doi.org/10.3390/antiox10030345
- For functional annotation part: To be submitted.
- For metagenome part:
Oec N & Bono H. Rapid metagenomic workflow using annotated 16S RNA dataset. BioHackrXiv
https://doi.org/10.37044/osf.io/gbt8p