What it does

Inference of differential exon usage in RNA-Seq.

Inputs

DEXSeq takes count tables generated from the dexseq_count as input. Count tables must be generated for each sample individually. DEXSeq is capable of handling multiple factors that affect your experiment. The first factor you input is considered to be the primary factor that affects gene expressions. You can also input several secondary factors that might influence your experiment but the final output will be changes in genes due to primary factor in the presence of secondary factors. Each factor has two levels/states. You need to select an appropriate count table from your history for each factor level.

The following table gives some examples of factors and their levels:

Note: Output log2 fold changes are based on primary factor level 1 vs. factor level 2. Here the order of factor levels is important. For example, for the factor 'condition' given in the above table, DEXSeq computes fold changes of 'Knockdown' samples against 'Wildtype', i.e. the values correspond to up or down regulations of genes in Knockdown samples.

Output

DEXSeq generates a tabular file containing the different columns and an optional html report. It can also ouput the DEXSeqResults R object that can be used with the plotDEXSeq tool to visualise individual genes.