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