Tool for obtaining counts for paired-end strand specific RNAseq data?

[JenBarb]

Does anyone have any suggestions for software tools to obtain counts for paired-end Strand-specific RNA-seq data? I used Tophat for my genome alignment and need a counting tool now to align to a reference transcriptome. I have tried coverageBed and Htseq-count. CoverageBed does not treat my paired end data properly and htseq-count seems to only work on my some of my samples and not all. Any other tools out there to use on this type of rna-seq data?

[Simon Anders]

Could you explain what you meant by "reference transcriptome"?

[JenBarb]

I mean a file with defined transcripts and their corresponding exon coordinates to use with the counting software.

The tophat output gives my reads mapped to the entire genome (mm10 in this case) then for the next step, I use a transcriptome file that has defined transcripts with exon coordinates. I am interested in obtaining read counts that align to each transcript or to each transcripts exons in the file.