How to create count table for SOAP output?

[ahmadsam]

Hi
I would like to use SOAP to align RNA-Seq reads with Rice genome, i have 2 questions :

1- How can i use GTF gene annotation file in SOAP ? (and which version?)
2-How can i create Count table for SOAP output (any software) ?

thanks

[Brian Bushnell]

Soap is not designed for RNA-seq alignment, and it does not use GTF files. You'd be better off using a splice-aware aligner such as BBMap, TopHat, or Star.

For determining gene expression, many people use Cufflinks.