Is There Any Softwares Can Create Exon-Exon Junction Database For Rna-Seq Mapping?

Question

[Gangcai]

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

Answer 1

[Fred]

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

[Gangcai]

I have checked the scripts, it only uses the Ensembl database through Ensembl API. But in my case, the gene annotation is only available in sanger database.

[Gangcai]

Thanks for your quick reply, I will look at it~

[Fred]

I don't know other tools that does that. You may have to wrote your own Junction database "maker". For small exons, the combinatorial may be too big, especially for genes with large number of exons. In this particular case, you can limit the search to known junctions.