Multivariate Analysis of Transcript Splicing (MATS)

Xing Lab, University of California, Los Angeles

Create junction annotation with user defined junction length:

Run createJunctionAnnotation.sh with the following format
./createJunctionAnnotation.sh -d database -o output_folder -j halfJunctionLength -p pygrStationPATH -s species

-d option takes either knownGene or Ensembl
The database is constructed from all possible junctions in either UCSC knownGene transcripts (hg19) or Ensembl transcripts (release 57 for hg19, release 65 for mm9). The junctions are generated by every possible exon combination within their respective gene annotation.

-s option takes either hg19 or mm9
hg19 is for human and mm9 is for mouse

-p option specifies the path to pygrStation
pygrStation contains three files per species (sequence itself, .pureseq, and .seqlen)

The resulting fasta and bowtieIndex will be in the user-specified output_folder.

e.g)
./createJunctionAnnotation.sh -d knownGene -o knownGene_hg19_50 -j 25 -p /Path/to/pygr/hg19/ -s hg19
./createJunctionAnnotation.sh -d Ensembl -o Ensembl_mm9_50 -j 25 -p /Path/to/pygr/mm9/ -s mm9