i am planing to use GS FLX + system for crow transcriptome sequencing . how many sample i can pooled to get minimum coverage of 5x or more than that. its necessary to focus minimum coverage for effective transcriptome analysis or any other option are available.
Transcriptome coverage is very difficult to do properly, since RNA is present in very variable amounts, and it is difficult to get libraries where all transcripts are expressed. Normalization helps somewhat, but you may lose some genes entirely in the process, and in any case, it won't help you get transcripts that weren't present in the libraries.
So, no, I don't think you will be able to get 5x coverage for the complete transcriptome. The best you can do is to use a large variety of libraries, including early developmental stages and immunostimulated ones, and sequence as much as you can.
PS: Why not Illumina? It'll give you more sequence at lower cost.