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| The iPlant CyVerse App Store is currently being restructured, and apps are being moved to an HPC environment. During this transition, users may occasionally be unable to locate or use apps that are listed in our tutorials. In many cases, these apps can be located by searching them using the search bar at the top of the Apps window in the DE. To increase the chance for search success, try not searching the entire app name and version number but only the portion that refers to the app's function or origin (e.g. 'SOAPdenovo' instead of 'SOAPdenovo-Trans 1.01'). In critical cases, please report your concern to the iPlant Ask forum or to support@iplantcollaborative.org. Thank you for your patience. |
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Author: Zhenyuan "Jerry" Lu (luj at cshl.edu) / iPlant CollaborativeCyVerse, Cold Spring Harbor Laboratory
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For more information see this page.
Prerequisites
- An iPlant accountCyVerse account. (Register for an iPlant account at a CyVerse account at http://user.iplantcollaborativecyverse.org.)
- The DE Quick Start tutorial provides an introduction to basic DE functionality and navigation.
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- Log into the Discovery Environment: https://de.iplantcollaborative.org/de/.
- Open the Bowtie-2.2.1-Build-and-Map app (Apps > Public Apps > NGS > Aligners > Bowtie-2.2.1-Build-and-Map).
- Name your analysis (Sample data: Leave default name for sample data).
- Select an "output folder" (Sample data: Leave default folder, "analyses").
- Click on the "Reference Index" tab.
- There are three options to upload a reference index, either SELECT a reference sequence from a drop down menu, INPUT a reference sequence fasta from the iPlant data CyVerse data store OR INPUT an archived set of index files (also from the data store) for your reference. For sample data, input a reference sequence.
- For the sample data click "Browse" under the "Reference fasta" field and select Community Data > iplantcollaborative > example_data > bowtie > e_coli.fa.
- Click on the "Inputs" tab.
- Enter a fastq file. (Sample data: Community Data > iplantcollaborative > example_data > bowtie > e_coli_10000snp.fq)
- Click "Launch Analysis".
- Once the analysis is complete (less than 5 minutes with sample data), select the output file generated (Sample data: "Bowtie-2.2.1-Build-and-Map_analysis1" folder found in "analyses"). The output file is called "BowtieOut.sam". The output is in SAM format, the human readable equivalent of a BAM file. For more information on SAM files see http://samtools.github.io/hts-specs/SAMv1.pdf.
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- Phytozome: database for multiple plant genomes at JGI in Walnut Creek, CA. JBrowse can be found under "Tools" at the top of the page.
- CoGe: comparative genomics platform, powered by iPlantCyVerse. To view variants in CoGe, click on "What do you want to do?," then on "LoadExperiment" (Documentation). Once the data is loaded click on "Continue to ExperimentView". On the ExperimentView page, click on "View" to be taken to the genome browser.
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