Figure 4

Assessment of the strand-specificity of the RNA-Seq library. The strand specificity of the sequencing library was based on comparing the number of first-in-pair reads mapped to the plus strand, to the corresponding number of second-in-pair reads. In a strand-specific library, the strand-specific log ratio (SSLR) should be away from zero. In the protocol used in this study, where the second-in-pair read comes from the sense strand, a negative SSLR is expected. (A) The distribution of SSLRs for putative transcripts having at least one proper read pair mapping to them demonstrates a preference for those with a negative SSLR. (B) When the plot is limited to those with twenty read pairs mapping to them, the bimodal distribution becomes more distinct, likely from the removal of contigs arising from contaminating genomic DNA.