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IsoEM2 (version 1.0.0)

Sample name:

Output files label

Will you upload a reference transcriptome fasta file from your history or use a built-in reference?:

Built-ins were indexed using default options

Select a reference dataset:

If your reference of interest is not listed, contact the Galaxy team

Select RNA-seq type:

RNA-Seq file, fastq format:

m (RNA-Seq fragment length mean):

d (RNA-Seq fragment length standard deviation):

Min. read length:

What it does

IsoEM2 infers isoform and gene expression levels (along with bootstrapping based confidence intervals) from high-throughput transcriptome sequencing (RNA-Seq) data.

Input Format

The IsoEM2 tool can process RNA-seq reads generated by both Ion Torrent and Illumina platforms. RNA-Seq reads must be provided in fastq format.

Output Format

IsoEM2 generates four output files containinag results for Isoform FPKM, Isoform TPM, Gene FPKM, and Gene TPM. The four tab delimited files have identical format, including the following fields:
1- Isoform/Gene ID
2- Isoform/Gene FPKM (Fragments Per Kilobase per Million reads) or TPM (Transcripts per Million reads)
3- Lower-bound for the 95% confidence interval of the Isoform/Gene FPKM/TPM estimate determined by bootstrapping
4- Upper-bound for the 95% confidence interval of the Isoform/Gene FPKM/TPM estimate determined by bootstrapping
5- A compressed tar archive containing bootstrap samples used to determine confidence intervals. These archives can be used as input to the IsoDE2 tool for computing differentially expressed isoforms/genes.

BUILT-IN REFERENCES

All reference files used in this pipeline can be found at http://dna.engr.uconn.edu/tmp/galaxy/tool-data/IsoEM.loc