G) Combine mapping outputs

Combine mapping outputs (app: Concatenate Multiple Files)

Description: The Concatenate Multiple Files app joins files head to tail. It's useful for combining data files, adding headers to files, and a host of other purposes. In this workflow the app is being used to connect multiple output files form the mapping operation in Section F (Map transcripts), which resulted from splitting the reference sequence FASTA files in Section E (Split RefSeq file). The app is a wrapper for the UNIX command 'cat'. Documentation: http://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html.

1. Log into the Discovery Environment: https://de.iplantcollaborative.org/de/.
2. Open the Concatenate Multiple Files app (Public Applications > General Utilities > Text and Tabular Data > Concatenate Multiple Files).
   1. Change 'Analysis Name' to Combine_Mapping_Outputs, add a 'Description' (optional), and use the default 'output folder'.
3. Click on the Select input data tab.
   1. Click on 'Add' under the 'Input Files' field. Browse to the folder that holds the output files from the BLAT analysis and enter the mapped transcript files from Section F (Map transcripts) in the correct order (Sample data: Community Data > iplant_training > rna-seq_without_genome > G_combine_mapping_outputs > BA_trnsPep_v_refseq0.psl; then select BA_trnsPep_v_refseq1.psl, and BA_trnsPep_v_refseq2.psl).
4. Click on "Launch Analysis".
5. Click on 'Analyses' from the DE workspace and monitor the 'Status' of the analysis (e.g., Idle, Submitted, Pending, Running, Completed, Failed).
   1. Once launched, an analysis will continue whether the user remains logged in or not.
   2. Email notifications update on the analysis progress; they can be switched off under 'Preferences'.
   3. If the analysis fails or does not proceed in the anticipated timeline, check these tips for troubleshooting. (Using the sample data, the analysis should be complete in less than 5 minutes.)
   4. To re-run an analysis, click the analysis "App" in the 'Analyses' window.
6. Access analysis results in one of two ways:
   1. In the 'Analyses' window click on the analysis "Name" to open the output folder.
   2. In the 'Data' window, click on user name, then navigate to the folder that holds the output of the analysis. (Find the output for the sample at Community Data > iplant_training > rna-seq_without_genome > G_combine_mapping_outputs > output_from_sample_data.)
7. The output file will be named concatenate_out.txt.