When viewing RNA-seq data against the genome, there are often short regions that have no reads in them. This is probably caused by fragmentation not being uniform. It causes unavoidable problems for transcript isoform assembly. Has anyone had the opportunity to examine if technical replicates of the same biological sample are made, except for varying the sonication time, and the results of sequencing are pooled, whether that improves RNA-seq assembly ? I hope that fragments that were obliterated would be present in the samples with shorter sonication times, and using a spectrum of sonication times could capture a better representation of fragments.
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Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
