Use FastQC and Trimmomatic to perform the quality control of your samples, to filter reads and to remove low quality bases.
Assemble short reads with Trinity to obtain a de-novo transcriptome without a reference genome. Assess the completeness of the transcriptome with BUSCO, cluster similar sequences with CD-HIT, and predict coding regions with TransDecoder.
Align RNA-seq data to your reference genome making use of STAR (Spliced Transcripts Alignment to a Reference) or BWA (Burrows-Wheeler Aligner). Regardless or your hardware in the OmicsBox Cloud.
Quantify expression at gene or transcript level through HTSeq or RSEM and with or without a reference genome.
Detect differentially expressed genes between experimental conditions or over time with well-known and versatile statistical packages like NOISeq, edgeR or maSigPro. Rich visualizations help to interpret results.
By combining differential expression results with functional annotations, enrichment analysis allows to identify over- and underrepresented biological functions.
SKU | transcriptomics |
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Status | Enabled |