How to calculate RPKM of de novo assembled sequences

[zinky]

I got some single reads produced by illumina ,and it's assembling sequences by Trinity; I want measure those seqs RPKM（which indicates expression number）,is their any software can do this;?
ps:without refGenome.

[kopi-o]

Trinity outputs an FPKM value for each contig; look in the FASTA headers.

[zinky]

thanks for your answer,i notice this FPKM value,but i want to compare two samples's expression number with significant pvalue calculated by statistic Test(such as Possion Test). as far as i know,this p-value can only be produced through process of counting mapped reads of which kind of data Trinity has no output .anyway,thanks all the same.hoping further reply.

[kopi-o]

OK, then you might want to check out the recommended workflows for that on the Trinity page, for instance map bacK the reads to the contigs, use RSEM (or some other program) to calculate counts and FPKMs, and run something like edgeR

http://trinityrnaseq.sourceforge.net/analysis/diff_expression_analysis.html

[zinky]

It's very kind of you !this seems useful to me ,i'll try frist!