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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Rationale:

Have you run Evolinc many times on a lot of different tissues and want to generate a final updated genome annotation file (GTF) and FASTA of lincRNAs for your species of interest? This app accomplishes that by searching through a folder and all of its subdirectories to find the "updated.gtf" from each Evolinc run. It then merges all of those GTFs into one "Final_updated.gtf" alongside the known genes for that species. It also generates a FASTA file containing all the lincRNA sequences. Importantly, the Evolinc output GTFs can all have the same name as long as they are in unique sub-directories. For instance, within the folder "Evolinc_output" you can have the sub-directories "Evolinc_output\Run_1\lincRNA.updated.gtf" and "Evolinc_output\Run_2\lincRNA.updated.gtf". Both "lincRNA.updated.gtf" files will be recognized and merged into one in the end. This is useful if you have many analyses that you would like to merge into one annotation file. The FASTA sequence file can be used directly with Evolinc-II.

Evolinc_merge-1.0 is invoked using the following:

  1. Input (s)
    1. Folder where all of the updated GTFs are located (they can be in subfolders)

    2. GTF that was used as input for RMTA - not Evolinc
    3. Original genome (.fasta) used in Evolinc or RMTA
  2. Outpus
    1. FASTA file containing all the lincRNA sequences 

    2. Merged gtf file (Final_updated.gtf)

Please work through the documentation and add your comments on the bottom of this page, or email comments to support@cyverse.org. Thank you.

Test Data

 The test data for Evolinc_merge-1.0

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All files are located in the Community Data directory of the iPlant Discovery Environment at the following path: Community Data > iplantcollaborative > example_data > Evolinc_merge (/iplant/home/shared/iplantcollaborative/example_data/Evolinc_merge/)

Run Evolinc_merge as following:

  1. Input (s)
    1. - Evolinc_merge folder that contains 2 sub-folders 676_120604.evolinc.out and 674_120530.evolinc.out)
    2. Homo_sapiens.GRCh38.dna.primary_assembly.fa
  2. Outpus
    1. Final_updated.gtf and Updated_lincRNAs.fa

Tool Source for App