People need to use this tool (ISAVASE) to identify alternate splicing locations and Exonic splicing enhencer (ESE) regions and Exonic splicng silencer (ESS) regions, but what's about this tool is an article (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1732-7#author-information) and this description (https://sourceforge.net/projects/isvase/files/) which is not so detailed and that generates doubts, such as:
In the code I need to use -rv or is it optional ???
Codigo: perl perl/ISVASE.pl -g genome_sequence(fasta) -dv database_of_dna_variant(VCF) -rv database_of_rna_editing(RADAR/DARNED) -s sam_file(SAM) -an annotation_file(GTF, GFF or BED) -k known_junction_association_identifcation(yes or no) -q minimum_quality -l minimum_read_length -d minimum_read_depth -c minimum_allele_depth -a minimum_anchor_size -p minimum_alt_proportion -f fisher_exect_test(pvalue) -o prefix_of_out_file.
If anyone has already used this tool, please share the experience, informed if it is easy to use, if any problems occurred during the execution and if you can share the script I appreciate it.
Thank you
