Frequently Asked Questions

What is Supersplat?

Supersplat is an application for discovering potential splice junctions in high throughput sequencing (HTS) data. It does this by virtue of Doug's brilliance, in which it is able to pick out splice junctions amidst the enormous number of genomic reads.

Supersplat's primary parameters indicate the Fasta-formatted reference file (-r) and the Fasta-formatted high-throughput (HTS) reads file (-f) on which supersplat will operate. Given these data, supersplat mines the references for all potential splice junctions indicated by the HTS reads, constrained by the minimum intron size (-n) and maximum intron size (-x) specified. Supersplat can>generate a large amount of output, on the order of tens or even hundreds of gigabytes. Methods for reducing the size of supersplat's output will be discussed below.

Supersplat works by partitioning each read into all possible two-chunk sizes, given minimum read>chunk size (-c), and searching over each reference for locations where both chunks exactly match the reference, within given minimum intron size (-n) and maximum intron size (x). For example, given the short-read ACTGACTGACTG and -c = 3, supersplat begins by partitioning the read as:

ACT GACTGACTG

Supersplat then searches the reference for ACT within appropriate distance to GACTGACTG. All locations found are reported. Next, supersplat partitions the read as:

ACTG ACTGACTG

Supersplat then searches the reference for ACTG within appropriate distance to ACTGACTG. Again, all locations found are reported. This process repeats until supersplat partitions the read as:

ACTGACTGA CTG

>Supersplat identifies potential introns by locating positions within the reference sequence which>match these read-chunks.

What kind of input can I use Supersplat on?

Supersplat takes a fasta file of the reads and the high-throughput sequencing file in order to mine for splice junctions.

How does Supersplat work

For all of the details you can read the paper Supersplat was published in. But, in short, it just knows what to do

Will you do my analysis for me?

If you bring Doug donuts.