Do the default parameters of Bowtie2 (sensitive: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode)) provide good enough results to publish for assembling Illumina HiSeq unpaired 101 bp reads to a reference chloroplast genome? I don't know how to change parameters and wouldn't know what to change them to even if I could. The default parameters seem to be giving good results. Any suggestions?
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It kind of depends on the question you are trying to answer. obviously. But I would say the answer is yes, there's no pressing need to change the params unless you have a specific reason to. It's fairly key to know the % of reads that have mapped successfully, and it's also worth examining the alignment (e.g. samtools tview or a windowed viewer like Tablet) to check there are no obvious misalignments.
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The immune system’s power comes from its genetic diversity, allowing myriad threats to be neutralized through first recognizing foreign antigens. That diversity is also what makes the immune system so difficult to study. Recent advances in sequencing technology and computational biology, however, are giving researchers new tools to understand immune responses and immune-related diseases in greater detail.
This convergence of genetics, immunology, and computation...09-01-2026, 05:41 AM
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