Set Analysis Parameters

Set Analysis Parameters

1 Navigate to BaseSpace, and then click the Apps tab.
2 In Categories, click RNA-Seq, and then click RNA-Seq Alignment.
3 From the drop-down list, select version 1.0.0, and then click Launch to open the app.
4 In the App Session Name field, enter the analysis name.

By default, the analysis name includes the app name, followed by the date and time that the analysis session starts.

5 From the Save Results To field, select the project that stores the app results.
6 From the Samples field, browse to the sample you want to analyze and select the checkbox.

You can analyze multiple samples. Select the checkbox to identify samples prepared with the TruSeq Stranded Total RNA and TruSeq Stranded mRNA library prep kits for the first strand and the ScriptSeq v2.0 RNA-Seq library prep kit for the second strand.

7 From the Reference Genome field, select the reference genome to be used for alignment. The default is Homo sapiens (PAR-masked)/hg19 (RefSeq).
8 From the Panel field, select from the following:
None (default)
TruSight RNA Pan-Cancer

The TruSight RNA Pan-Cancer library prep kit only supports the Human, UCSC hg19 (RefSeq & Gencode) reference genome.

9 From the Aligner field, select from the following methods:
STAR (default)
TopHat (Bowtie)
TopHat (Bowtie2)
10 [Optional] Select the QC Mode checkbox . If selected, enter the number of read pairs for each sample.
11 [Optional] Select the Novel Transcript Assembly checkbox for Cufflinks to assemble novel transcripts. If selected, select the Adjust Transcript Assembly for Samples Without PolyA Selection checkbox if the samples are prepared without PolyA selection (TruSeq Total RNA kit).


By default, the Call Fusions checkbox is checked if you selected a panel and an aligner that supports fusion calling. Paired-end reads are required. The TopHat (Bowtie) aligner supports TopHat-fusion. The STAR aligner supports Manta-fusion. The TopHat (Bowtie2) aligner does not support fusion calling. For best results, use the STAR aligner with the TrusSight RNA Pan-Cancer panel.

12 From the ERCC Spike-In Controls field, select from the following options:
None (default)
Mix 1
Mix 2
13 [Optional] Select the Trim TruSeq Adapters checkbox.

This option trims adapter sequences from the FASTQ file. Use this option if adapter trimming was not performed in the demultiplexing.

14 [Optional] Select the Set Advanced Options checkbox to enable the advanced options and then specify the values for the appropriate options. See Advanced Options.
15 Click Continue.

The RNA-Seq Alignment App begins analysis.

When analysis is complete, the app updates the status of the session and sends an email to notify you.