The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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RMTA is a wrapper script built on top of several publicly available bioinformatic tools that can rapidly proceed from raw short read data to assembled transcripts. RMTA performs this by mapping reads using either HiSat2 or Bowtie2 and then assembling transcripts using either Cufflinks or StringTie according to user preference. RMTA can process FASTQ files containing paired-end or single-end reads or can directly process one or more sequence read archives (SRA) from NCBI using SRA IDs. RMTA has been successfully used by many groups as the first step towards the identification of long non-non coding RNAs using the Evolinc workflow. More information about RMTA can be found here

The OSG is a consortium of research communities which facilitates distributed high throughput computing for scientific research. The Open Science Grid (OSG) enables distributed computing at more than 120 institutions, supports efficient data processing and provides large-scale scientific computing of more than 2 million CPU hours per day. More about OSG can be found here

OSG-RMTA (read mapping, transcript assembly), is a gene quantification workflow for RNA-Seq data utilizing CyVerse’s Discovery Environment HT-Condor for job submission , and Datastore for data management and OSG for distributed high throughput computing.

RMTA minimally requires the following input data: