Reads were uniquely mapped to >35,000 genes in each species, with unique read counts per gene ranging from 1 to >98,000, reflecting the relative abundance of that transcript in the transcriptome (Marioni et al. 2008).
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Briefly, a perl script scans through all of the sequence outputs and assigns a copy number for each unique read.
We considered both alignment locus and read length in our definition of read duplication, allowing one read at each locus with a unique read length.
Using the relative proportion of the total unique read counts against total number of reads, a condition tree (Genespring 7.3.1, Agilent) of all novel candidates plus known miRNAs gave good separation of the different histological subtypes of sample (Figure 3).
We used SAMtools v0.1.19 (flagstat) to compile the unique read alignment rate per sample.
Pathoscope has a thetaPrior parameter that enforces a unique read penalty.
The optimal read in SWA is the unique read with longest overlapped bases.
Mate pairs with correct orientation on the transcript and unique read placement were retained.
In SWA, each extension requires a unique read, called a seed, to initiate the extension.
