I am dealing with some RNA-seq data. First, I assemblied the short reads to contigs using Trinity, and then map the short reads to the contigs using BWA. I would like to get ungapped alignment from BWA by setting -o to 0 and other parameters as default. However, I still got gapped alignment. So my question is: what parameter should I set to get ungapped alignment from BWA. Thanks in advance!
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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...
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