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:

The program gffread can be used to validate, filter, convert and perform various other operations on GFF files. Because the program shares the same GFF parser code with Cufflinks, Stringtie, and gffcompare, it could be used to verify that a GFF file from a certain annotation source is correctly "understood" by these programs. Thus the gffread utility can be used to simply read the transcripts from the file, and optionally print these transcripts back, in either GFF3 (default) or GTF2 format (with the -T option), while discarding any non-essential attributes, optionally fixing some potential issues with the input file(s)

gffread is invoked using the following:

  1. Input (s)
    1. Full path to a multi-fasta file with the genomic sequences for all input mappings (reference genome - can either be a custom or a reference genome from DE).

    2. The annotation file (gtf file)
  2. Outpus
    1. Fasta file with spliced exons for each GFF transcript (Default - output.fa)

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 gffread-2.2.1 consists of a sample gtf file and 1st chromosome from Arabidopsis thaliana 

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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 > gffread (/iplant/home/shared/iplantcollaborative/example_data/gffread/)

Run SplAdder as following:

  1. Input (s)
    1. Sample gtf file - Sample_cuffcompare_out.gtf
    2. Chromosome 1 fasta file - TAIR10_chr1.fasta
  2. Outpus
    1. output.fa fasta file with spliced exons for each GFF transcript

 

Tool Source for App