A) Eliminate small transcripts

Eliminate small transcripts (app: Select contigs)

Description: Select contigs is an app that selects contigs of a minimum length from a set of contigs. Documentation: https://pods.iplantcollaborative.org/wiki/display/DEapps/Select+contigs.

1. Log into the Discovery Environment: https://de.iplantcollaborative.org/de/.
2. Open the Select contigs app (Apps > Public Apps > NGS > Assembly Annotation > Select contigs).
   1. Change 'Analysis Name' to Limit_Transcripts_300, add a 'Description' (optional), and use the default 'output folder'.
3. Click on the Main settings tab.
   1. Click on the 'Input fasta file' field. Browse to the folder that holds the FASTA file containing the contig sequences (Sample data: Community Data > iplant_training > rna-seq_without_genome > A_eliminate_small_transcripts > soaptrans25.scafSeq).
   2. Select the FASTA file, then click on OK.
   3. Click in the 'Output fasta file name' field. Rename 'selected_contigs.fa' to 'BAtranscriptome_300andup.fa'.
4. Scroll down and click on the options tab.
   1. Click in the 'Minimum contig size' field and enter 300.
5. Click on "Launch Analysis".
6. 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 min.)
   4. To re-run an analysis, click the analysis "App" in the 'Analyses' window.
7. 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 > A_eliminate_small_transcripts > output_from_sample_data.)
8. Compare the size of the output file against the size of the input fasta file. The size of the output file can be expected to be smaller, as Select contigs will likely have eliminated contigs below the threshold size of 300.