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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NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM
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