Hi
"I am conducting transcriptome analysis on a parasitic plant for which no whole genome is available. I would appreciate assistance in suggesting steps for analysis after Trinity assembly, including differential expression analysis, identification of coding sequences (CDSs), KEGG pathway analysis, and other relevant analyses.
Thank you for your suggestions
Samvedna Singh
Hello,
These are some crucial steps that must be followed during RNA seq analysis. Hope it helps.
Steps:
- RNA Isolation
- RNA Quality Assessment
- Library Preparation
- Sequence the prepared libraries using next-generation sequencing (NGS) platforms such as Illumina or PacBio. Generate raw sequencing data (reads) in FASTQ format.
- Quality Control of Sequencing Data
- Pre-processing
- Transcriptome Assembly
- Annotation and Functional Analysis
- Compare the expression levels of transcripts between different experimental conditions or tissues using tools like DESeq2, edgeR, or limma. This step helps identify differentially expressed genes and pathways.
- Validation using experimental techniques such as qRT-PCR or RNA-seq validation experiments.
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