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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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