Question: Is There Any Softwares Can Create Exon-Exon Junction Database For Rna-Seq Mapping?
2
gravatar for Gangcai
7.9 years ago by
Gangcai230
Berlin Or Shanghai
Gangcai230 wrote:

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

ADD COMMENTlink modified 7.7 years ago by Fred700 • written 7.9 years ago by Gangcai230
3
gravatar for Fred
7.9 years ago by
Fred700
Paris, France
Fred700 wrote:

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

ADD COMMENTlink written 7.9 years ago by Fred700
1

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.

ADD REPLYlink written 7.9 years ago by Gangcai230

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

ADD REPLYlink written 7.9 years ago by Gangcai230

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.

ADD REPLYlink written 7.9 years ago by Fred700
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