How Can Gene Expression Levels of Specific Genes Be Quantified Across Different Species in Transcriptome Sequencing?
To quantify the expression levels of specific genes across different species, the following approach can be applied:
1. Quality Control and Data Cleaning
Begin by assessing the raw sequencing data (FASTQ files) using quality control tools such as FastQC to evaluate sequencing quality, duplication levels, adaptor contamination, and other technical artifacts.
Based on the quality reports, employ sequence trimming tools like Trimmomatic or cutadapt to remove low-quality sequences, adaptors, and other contaminants.
2. Read Alignment
Select an appropriate reference genome and/or transcriptome for each species under study, and download the corresponding sequence and annotation files. Since different species are involved, a species-specific reference must be used for each case.
Align the cleaned reads to the respective reference genomes using alignment tools such as HISAT2, STAR, or Bowtie2. This step generates SAM or BAM files that contain detailed information about how the reads map to the reference genome.
3. Quantification
Use transcriptome-specific quantification tools like HTSeq or featureCounts to extract gene expression counts from the alignment files. These tools calculate read counts for each gene by determining how many reads align to the annotated regions of each gene in the reference genome.
MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider.
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