What it does

IsoDE2 computes isoforms and genes that are differentially expressed between two conditions (e.g., treated vs. control). The computation is based on the boostrap samples generated by IsoEM2.

Input

• 1- Names for the two conditions (the default values 'Condition 1' and 'Condition 2' will be used in the output file names if these are not specified)
• 2- One or more IsoEM output files (compressed tar files) for each of the two conditions. Multiple files can be used when IsoEM2 is run independently on replicates for each condition.
• 3- Desired significance level for which a reliable fold change level will be reported.

Output

• Four output files containinag results of isoform and gene differential expression analysis based on both Fragments per Kilobase per Million (FPKM) and Transcripts per Million (TPM) expression levels. The four tab delimited files have identical format with the following fields:
• 1- Isoform/Gene ID
• 2- Confident log_2(FC): the base 2 logarithm of the largest fold change of isoform/gene FPKM/TPM estimates of condition 2 vs condition 1 which is supported by the provided bootstrap samples at the specified significance level. Positive values represent over-expression in Condition 2, while negative values representing over-expression in Condition 1. A zero value in this field indicates that no significant change was detected.
• 3- Single run log2(FC): the base 2 logarithm of the ratio between expression levels estimated by IsoEM2 for Condition 2 and Condition 1 (ratio between mean estimates in case replicates are provided for the two conditions).
• 4- Condition 1 FPKM or TPM: the IsoEM2 expression level estimated for Condition 1 (mean value in case of replicates).
• 5- Condition 2 FPKM or TPM: the IsoEM2 expression level estimated for Condition 2 (mean value in case of replicates).