ASprofile consists of several programs for extracting (extract-as), quantifying (extract-as-fpkm) and comparing (collect-fpkm) AS events from transcripts assembled from RNA-seq data in multiple conditions, e.g. tissues.
The first program, extract-as, takes as input a GTF transcript file, such as that created by Cufflinks, and compares all pairs of transcripts within a gene to determine exon-intron structure differences that indicate an AS event. To determine AS events among multiple samples, the input file should be the concatenation of the transcript files of individual samples, with the gene names reconciled across the samples to allow comparison. The same event may be discovered and reported multiple times, from different transcripts. For this reason, we recommend that you run the script summarize_as to create a non-redundant listing (catalog) of all events. This format is also required for the rest of the programs in the ASprofile suite.