I'm looking for the best way to find novel variants in RNA-seq data independent of a expectation of ploidy (i.e from RNA-editting, etc.)
Illumina HiSeq 2000 sequencing. About 20 million reads per sample. Human samples so the ref genome is known. I have tried GATK Unified Genotyper but it overcalls.
you can also try samtools and MISO (http://genes.mit.edu/burgelab/miso/)
Adherent tumor-derived cells in 96-well plates. Want to measure a highly expressed gene and a housekeeper.
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