Sequence list of unmapped reads

If you chose the option to Create a list of unmapped reads, then a sequence list of these will be produced. If you started with paired reads then more than one list of unmapped reads may be produced: paired reads are put in one list, with a name that ends in (paired), singe reads, including members of broken pairs, are put in a read list with a name than ends in (single).

Definition of RPKM
RPKM, Reads Per Kilobase of exon model per Million mapped reads, is defined in this way [Mortazavi et al., 2008]:

$\displaystyle \emph{RPKM} = \frac{\emph{total exon reads}}{\emph{mapped reads(millions)} \times \emph{exon length (KB)}}. $

For prokaryotic genes and other non-exon based regions, the calculation is performed in this way:

$\displaystyle \emph{RPKM} = \frac{\emph{total gene reads}}{\emph{mapped reads(millions)} \times \emph{gene length (KB)}}. $

Total exon reads
This value can be found in the column with header Total exon reads in the expression track. This is the number of reads that have been mapped to exons (either within an exon or at the exon junction). When the reference genome is annotated with gene and transcript annotations, the mRNA track defines the exons, and the total exon reads are the reads mapped to all transcripts for that gene. When only genes are used, each gene in the gene track is considered an exon. When an un-annotated sequence list is used, each sequence is considered an exon.
Exon length
This is the number in the column with the header Exon length in the expression track, divided by 1000. This is calculated as the sum of the lengths of all exons (see definition of exon above). Each exon is included only once in this sum, even if it is present in more annotated transcripts for the gene. Partly overlapping exons will count with their full length, even though they share the same region.
Mapped reads
The sum of all mapped reads as listed in the RNA-Seq analysis report. If paired reads were used in the mapping, mapped fragments are counted here instead of reads, unless the Count paired reads as two option was selected. For more information on how expression is calculated in this case, see Calculating expression values from RNA-seq. Please note that the option to Map to gene regions only will affect the number of mapped reads, since all intergenic reads will not be mapped if this option is selected. This means that comparison of RPKM values between samples should only be carried out if this parameter was set in the same way for all samples.