Alternative splicing analysis tool package (ASATP) includes a series of toolkits to analyze alternative splicing events, which could be used to detect and visualize alternative splicing events, check ORF changes, assess regulations of alternative splicing and do statistical analysis. You can process data in ASATP webserver ( http://systbio.cau.edu.cn/asatp ), or install ASATP into your local server.
- ASRecovist
Alternative splicing recognition and visualization tool, which is a program to detect alternative splicing events from a gene annotation and classified them into different types (CE, IR, MXE, A3SS, A5SS, AFE, ALE and other). Alternative splicing events will be showed in tables and graphs.
- ASQuantityDiff
Alternative splicing quantity comparison between samples, which was used to detect expression regulations of alternative transcripts.
- ASAffectORF
Check AS event in CDS region, to identify the effect of alternative splicing events for ORFs.
- runASATP
Run Alternative splicing Analysis Tool Package, which was a combined pipeline including ASRecovist, ASQuantityDiff and ASAffectORF.
- asp2bit
Transform AS pattern to bit matrix.
- bit2asp
Transform bit to ASP code.
- splitGtf
Split a GTF file when it's too large to process. Then you can process them separately using multi-CPU to save time.
ASATP works under Linux. To use ASATP, you need install Perl (>5.10). Some Perl modules are needed:
- Bioperl
- Bio::Graphics
- GD::Image
- GD::SVG
- Statistics::R
- Math::BigInt
You can use CPAN command to install modules needed. For example:
perl -MCPAN -e 'install Statistics::R'
To check whether ASATP work well, you can run commands like:
cd Sample
perl ../runASATP.pl --gtf anno.gtf --trExpFile isoform_exp.txt --output output_svg --graph yes --graphFormat svg
perl ../runASATP.pl --gtf anno.gtf --trExpFile isoform_exp.txt --output output_png --graph yes --graphFormat png
See "Full_documentation.pdf" in document folder.