L) Reformat mapping output

Reformat mapping output (app: SAM to sorted BAM)

Description: The SAM to sorted BAM app converts the SAM file output from Section K (Map RNA-Seq reads to transcripts) into their binary format, BAM files, and sorts the entries according to their map positions. This will allow counting the reads that map to each position in the transcriptome. Documentation: http://samtools.sourceforge.net/samtools.shtml.

1. Log into the Discovery Environment: https://de.iplantcollaborative.org/de/.
2. Open the SAM to sorted BAM app (Public Applications > NGS > SAMtools > SAM to sorted BAM).
   1. Change 'Analysis Name' to Reformat_Mapping_Output_con01, add a 'Description' (optional), and use the default 'output folder'.
3. Click on the Select input data tab.
   1. Enter each SAM output file from the previous section (Map RNA-Seq reads to transcripts) (Sample data: starting with BAcon01.sam) into the input for SAM to sorted BAM. Run each file on a separate job (Sample data: Community Data > iplant_training > rna-seq_without_genome > L_reformat_mapping_output > BAcon01.sam). Adjust the 'Analysis Name' accordingly (e.g. Reformat_Mapping_Output_con02 for the input file BAcon02.sam, etc.).
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 15 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 > L_reformat_mapping_output > output_from_sample_data.)