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OmicsBox Transcriptomics Module

SKU: transcriptomics

Availability: Out of stock

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transcriptomics

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TRANSCRIPTOMICS
Quality Control, Assembly, Quantification and Differential Expression
The OmicsBox Transcriptomics module allows you to process RNA-seq data from raw reads down to their functional analysis in a flexible and intuitive way.

Quality Control

Use FastQC and Trimmomatic to perform the quality control of your samples, to filter reads and to remove low quality bases.

De-Novo Assembly

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

RNA-Seq Alignment

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

Quantify expression at gene or transcript level through HTSeq or RSEM and with or without a reference genome.

Differential Expression Analysis

Detect differentially expressed genes between experimental conditions or over time with well-known and versatile statistical packages like NOISeqedgeR or maSigPro. Rich visualizations help to interpret results.

Enrichment Analysis

By combining differential expression results with functional annotations, enrichment analysis allows to identify over- and underrepresented biological functions.

Additional Information

SKU transcriptomics
Status Enabled