/
Modify_GFF_coordinates

Modify_GFF_coordinates

Jun 16, 2017

Rationale and background

Modify_GFF_Coordinates app will add bp to either side of the start and stop coordinates of the gff file. The user can select the delimiter (eg, gene, exon etc) as well as the number of base pairs to add to the gff file

Prerequisites

  1. A CyVerse account (Register for a CyVerse account at https://user.cyverse.org/).

  2. An up-to-date Java-enabled web browser. (Firefox recommended. If you wish to work with your own large datasets and upload them using iCommands, Chrome is not suitable due to its issues in utilizing 64-bit Java.)

  3. Inputs: 

    1. Input gff file: The path to the input gff file

    2. Delimiter: The feature of gff file that you want to add the bp to. Ex: gene)

    3. Base pairs: The number of base pairs to be added to either side of start and stop coordinates in the gff file

  4. Output File name: Name of the output file

Test/sample data

This tutorial uses the test data that is stored in the Data Store at Community Data > iplantcollaborative > example_data > Evolinc-I         

  1. Input:

    1. Input gff file: TAIR10_genes.gff

    2. Delimiter: gene

    3. Base pairs: 500

  2. Output File name: output.gff

Output

  1. logs

  2. Output

    1. output.gff