## How do I identify the specific reads that were incorporated into the transcript assemblies?

Currently, the mappings of reads to transcripts are not reported.  To obtain this information, we recommend realigning the reads to the assembled transcripts [Bowtie](http://bowtie-bio.sourceforge.net/index.shtml). Capturing both properly paired read alignments and single unpaired alignments can be captured and quantified as described [here](RNA-Seq-Read-Representation-by-Trinity-Assembly).