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Rationale and Background:

CLASS2: A fast and accurate alternative-splicing aware transcript assembler for RNA-seq reads aligned to a genome.

Song L, Sabunciyan S, Florea L. 2016. Nucleic Acids Res. 44(10):e98.  [ Medline ]

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The test data for CLASS2 can be found here: /iplant/home/shared/iplantcollaborative/example_data/class2

Test Run

1. Open CLASS2 in DE
2. Choose the input BAM file /iplant/home/shared/iplantcollaborative/example_data/class2/sample.bam
3. Optionally select the GTF annotation file /iplant/home/shared/iplantcollaborative/example_data/class2/sample.annot.gtf
4. Optionally set other parameters, such as Isoform fraction (-F) , Prefix for transcript names (-l) , Remove depth and splice files (–clean)  
5. Optionally set the prefix for the output file name
6. Launch the analysis
   
   

Test Results: 

1. sample.gtf:   Output file
2. If  selecting 'No' for the '--clean' option, then a folder named "class_tmp" containing alignment, splice junction and read coverage data will be generated. 
   

The following figure file illustrates the CLASS2 output for the test data, using the provided annotation:

sample.gtfclass_tmp.png