ASprofile is a suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data.
Download ASprofile here. The catalog of exon skipping events, as well as other types of events inferred from the Illumina Human Body Map data in sixteen human tissues and supporting data files for the comparative alternative splicing analyses, are here.
ASprofile -- extract and compare AS events from RNA-seq data from multiple tissues or conditions
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.
The following types of events are currently implemented: exon skipping (SKIP), cassette exons (MSKIP), alternative transcript start and termination (TSS, TTS), retention of single or multiple introns (IR, MIR), and alternative exon (AE). In addition, variations on these classes that allow for some 'wiggle' room at the boundaries of the surrounding features are also reported, prefixed with 'X'. For instance, a SKIP event requires the coordinates of the spanning intron in the exon-excluding isoform to precisely match the far ends of the two flanking introns in the exon-including isoform. An XSKIP event would simply require that the two flanking exons on each side of the skipped exon overlap. More details on the specific definitions employed can be found here.
The second program, extract-as-fpkm, calculates the FPKM of each event from those of transcripts harboring the event in a given sample, (optionally) allowing for a margin of error at the boundaries of the exons and introns.
Lastly, the script collect-fpkm collects the FPKM event values for all RNA-seq samples, and calculates and compares splicing ratios across samples. The results can be used to observe trends in the dynamics of AS profiles and select promising candidates for laboratory testing, but there is yet no rigorous statistical testing to assess their significance. We plan to add such a component in a future release.
ASprofile was written for Linux platforms. It may require some modifications to run on another Unix platform. ASprofile is still under development, so please write us with feedback and bug reports.
Download and unpack the gzipped tar file ASprofile.tar.gz.
gunzip < ASprofile.tar.gz | tar -xvf -
The tar will unpack into a directory named ASprofile.[version]. (You'll see what the precise name is while tar is unpacking.) Make that directory current.
Follow the instructions in the COMPILING file, included, to compile.
- Florea, L., L. Song and S.L. Salzberg (2013). Thousands of exon skipping events differentiate splicing patterns in sixteen human tissues [v1; ref status: awaiting peer review, http://f1000r.es/1p0] F1000Research 2013, 2:188 (doi: 10.12688/f1000research.2-188.v1).
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This work was supported in part by NSF grant ABI-1159078 to Liliana Florea and NIH grant R01-HG006677 to Steven L. Salzberg.