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I am dealing a set of RNA-seq data generated by Illumina, aligned and assembled by tophat-cufflinks pipeline. I wonder why so many of my non-code RNA expression values are zero, but not all of them?
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I"m guessing this is, for you, an early look at rnaseq results. Some genes are expressed, some aren't; this includes non-coding RNA. You'll see this as aligned reads with a gene (mostly the exons) and some genes have no alignments (meaning , likely, that they are not expressed or got filtered out during wet-lab processing). Some protocols only pick up polya mrna. If you can fully explain why some are lighting up and others aren't; then you got a paper.
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