I would like to compare the expression of two samples, one contains 60 million unpaired reads and the other contains 40 million unpaired reads and 20 million paired-end reads. What software would people recommend to use to find genes/transcripts that are differentially expressed? I have used tophat/cufflinks/cuffdiff on the unpaired reads. Can I use it utilize both paired and unpaired reads?
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
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