Rationale:
SplAdder, short for Splicing Adder, a toolbox for alternative splicing analysis based on RNA-Seq alignment data. Briefly, the software takes a given annotation and RNA-Seq read alignments in standardized formats, transforms the annotation into a splicing graph representation, augments the splicing graph with additional information extracted from the read data, extracts alternative splicing events from the graph and quantifies the events based on the alignment data, the quantified events can then be used for differential analysis. SplAdder in its default configuration, consists of the following steps:
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Test Data
The test data for Spladder-1.0.0 consists of 6 bam files and an annotation files from Arabidopsis thaliana
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All files are located in the Community Data directory of the iPlant Discovery Environment at the following path: Community Data > iplantcollaborative > example_data > spladder (/iplant/home/shared/iplantcollaborative/example_data/spladder/) |
Run SplAdder as following:
- Input (s)
- The folder containing the list of alignment files - /iplant/home/shared/iplantcollaborative/example_data/spladder/
- The genome annotation file (/iplant/home/shared/iplantcollaborative/example_data/spladder/TAIR10_GFF3_genes.tiny.gff)
- Parameters
- Alternative Splicing event type - Exon_skip, Intron_retention, alternate_3',alternate_5', multiexon_skip
- Confidence level - 3
- Primary_alignments_only - no
- Merge Strategy - merge_graphs
- OutpusOutputs
- Output folder containing the following files
merge_graphs_alt_3prime_C3.confirmed.pickle merge_graphs_alt_3prime_C3.counts.hdf5 merge_graphs_alt_3prime_C3.pickle merge_graphs_alt_5prime_C3.confirmed.pickle merge_graphs_alt_5prime_C3.counts.hdf5 merge_graphs_alt_5prime_C3.pickle merge_graphs_exon_skip_C3.confirmed.gff3 merge_graphs_exon_skip_C3.confirmed.pickle merge_graphs_exon_skip_C3.confirmed.txt merge_graphs_exon_skip_C3.counts.hdf5 merge_graphs_exon_skip_C3.pickle merge_graphs_intron_retention_C3.confirmed.pickle merge_graphs_intron_retention_C3.counts.hdf5 merge_graphs_intron_retention_C3.pickle merge_graphs_mult_exon_skip_C3.confirmed.pickle merge_graphs_mult_exon_skip_C3.counts.hdf5 merge_graphs_mult_exon_skip_C3.pickle
- Output folder containing the following files
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contig strand event_id gene_name exon_pre_start exon_pre_end exon_start exon_end exon_aft_start exon_aft_end NMD_DBL1.tiny:exon_pre_cov NMD_DBL1.tiny:exon_cov NMD_DBL1.tiny:exon_aft_cov NMD_DBL1.tiny:intron_pre_conf NMD_DBL1.tiny:intron_aft_conf NMD_DBL1.tiny:intron_skip_conf NMD_DBL1.tiny:psi NMD_DBL2.tiny:exon_pre_cov NMD_DBL2.tiny:exon_cov NMD_DBL2.tiny:exon_aft_cov NMD_DBL2.tiny:intron_pre_conf NMD_DBL2.tiny:intron_aft_conf NMD_DBL2.tiny:intron_skip_conf NMD_DBL2.tiny:psi NMD_WT1.tiny:exon_pre_cov NMD_WT1.tiny:exon_cov NMD_WT1.tiny:exon_aft_cov NMD_WT1.tiny:intron_pre_conf NMD_WT1.tiny:intron_aft_conf NMD_WT1.tiny:intron_skip_conf NMD_WT1.tiny:psi NMD_WT2.tiny:exon_pre_cov NMD_WT2.tiny:exon_cov NMD_WT2.tiny:exon_aft_cov NMD_WT2.tiny:intron_pre_conf NMD_WT2.tiny:intron_aft_conf NMD_WT2.tiny:intron_skip_conf NMD_WT2.tiny:psi Chr1 + exon_skip_1 AT1G21690 7616028 7616107 7616267 7616332 7616604 7616726 32.4 10.2 39.3 3 18 24 0.30 63.6 11.1 59.1 7 8 52 0.13 33.9 0.2 60.6 0 0 49 0.00 74.2 0.5 71.0 0 0 72 0.00 |