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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Comment: updated introduction

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Rationale and background:

RMTA is a wrapper script built on top of (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. RMTA is built using 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 IDsassemble and process either one's own single-end/paired-end RNA sequencing reads (FASTQ) or reads from the NCBI sequence read archive (SRA). RMTA maps reads to user-provided reference genome using either HiSat2 or Bowtie2, assembles transcripts using StringTie and performs read quantification using FeatureCounts. RMTA has been successfully used by many groups as the first step towards the identification of long non-coding RNAs using the Evolinc workflow. More information about RMTA can be found here

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.RMTA minimally requires the following input data:

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