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Old 03-26-2013, 10:24 AM   #1
Location: Bethesda, MD

Join Date: Oct 2010
Posts: 47
Default Tool for obtaining counts for paired-end strand specific RNAseq data?

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?
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