Transcriptomics and Expression
Some of the tools available for expression analysis
KBase offers a powerful suite of expression analysis Apps. Starting with short reads, you can use the tool suite to assemble and quantify long transcripts, identify differentially expressed genes, cluster them and analyze them as functionally enriched modules. You can also compare the expression data with the flux when studying metabolic models in KBase and identify pathways where expression and flux agree or conflict.

Reads Management

Reads Alignment

    Align Reads using Bowtie2 — aligns the sequencing reads for a set of two or more samples to long reference sequences of a prokaryotic genome using Bowtie2 and outputs a set of alignments for the given sample set in BAM format.
    Align Reads using TopHat2 — aligns the sequencing reads for a set of two or more samples to an eukaryotic genome using TopHat2 in order to identify splice junctions between exons with the help of Bowtie2 mapping program.
    Align Reads using HISAT2 — aligns the sequencing reads for a set of two or more samples to long reference sequences of a genome using HISAT2 and outputs a set of alignments for the given sample set or reads set in BAM format.

Reads Assembly

    Assemble Transcripts using Cufflinks — assembles transcripts for a given sample or a sample set using Cufflinks so that you can view the relative abundances of the assembled transcripts in a histogram, obtained as output from Cufflinks.
    Assemble Transcripts using StringTie — assembles transcripts for a given sample or a sample set using StringTie so that you can view the relative abundances of the assembled transcripts in a histogram.

Differential Expression

Last modified 9mo ago