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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flattenClusters 1.0

Community rating: ?????

A utility to map original Fasta Headers to clusterReport and/or queryOrthoMCL output.

Notes:

Quick Start

Test Data

Icon

Input test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> homolog_clustering -> 2_queryOrthoMCL_output
and
Community Data -> iplantcollaborative -> example_data -> homolog_clustering ->  4_Concatenate_Multiple_Files_output 

Output test data for this app appears directly in the Discovery Environment in the Data window under:
Community Data -> iplantcollaborative -> example_data -> homolog_clustering ->  13_flattenClusters_output

Input File(s)

Use 

Community Data -> iplantcollaborative -> example_data -> homolog_clustering -> 2_queryOrthoMCL_output -> Query.group

and

Community Data -> iplantcollaborative -> example_data -> homolog_clustering ->  4_Concatenate_Multiple_Files_output  -> Map_Combined.txt

Parameters Used in App

There are no parameters for this app.

Output File(s)

Expect 1 output file:

  1. A flattened.txt one sequence per line, each line with 3 tab-delimited fields:

(1)OrthoMCL cluster ID - (2)2-letter abbreviation from OrthoMCL v1.4  - (3)Original Fasta Header

Consider Community Data -> iplantcollaborative -> example_data -> homolog_clustering ->  13_flattenClusters_output  -> flattened.txt line 3:

(1)64 (2)PF (3)PF3D7_1468700 | organism=Plasmodium_falciparum_3D7 | product=eukaryotic initiation factor 4A (eIF4A) | location=Pf3D7_14_v3:2825370-2826918(+) | length=398 | sequence_SO=chromosome | SO=protein_coding

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