Dear all, Does anybody known any open source softwares which can create exon-exon junction database? And especially can deal with short exons(If the length of two exons is less than the length of reads, then the software need to add more exons for creating the junction).Thanks
In the Griffith paper ( http://www.nature.com/nmeth/journal/v7/n10/full/nmeth.1503.html ) they present their tool Alexa-Seq that can handle RNA-Seq data. I took a look at the code, and if I remember correctly, they have a script that makes Junction databases.
The script seems to be in alternativeExpressionDatabase/createExonJunctionDatabase.pl