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.
- Log into the Discovery Environment: https://de.iplantcollaborative.org/de/.
- Open the Concatenate Multiple Files app (Public Applications > General Utilities > Text and Tabular Data > Concatenate Multiple Files).
- Change 'Analysis Name' to Combine_Mapping_Outputs, add a 'Description' (optional), and use the default 'output folder'.
- Click on the Select input data tab.
- 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).
- Click on "Launch Analysis".
- Click on 'Analyses' from the DE workspace and monitor the 'Status' of the analysis (e.g., Idle, Submitted, Pending, Running, Completed, Failed).
- Once launched, an analysis will continue whether the user remains logged in or not.
- Email notifications update on the analysis progress; they can be switched off under 'Preferences'.
- 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.)
- To re-run an analysis, click the analysis "App" in the 'Analyses' window.
- Access analysis results in one of two ways:
- In the 'Analyses' window click on the analysis "Name" to open the output folder.
- 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.)
- The output file will be named concatenate_out.txt.