General Tips On Using Optimal Alignment Flags For Specific Data

Question

[blake.mcmurray]

Hello,

I am working with uncultured metagenomic data, trying to tease out 16s reads from raw reads and am pretty unfamiliar with how I might go about this optimally. I am using both bowtie2 and bwa and would like any general advice (or specific advice if you may have any) regarding how to go about running alignments with optimal flags and in general, learning how to use aligners more effectively. I have tried reading the docs of these aligners, but find it somewhat overwhelming to peruse and remember. Any advice or strategies would be greatly appreciated.

Kind regards,

Blake

[Istvan Albert]

You need to be more specific on what the goals are, beyond just stating

trying to tease out 16s reads from raw reads

that goal is insufficient to provide advice on using aligners.

That being said, in some cases there is little to almost no difference between the aligners even when used with default parameters. In other cases, depending on the data and error rates, each needs to be tuned.

Formulate your requirements with more detail - in addition do run the aligners and see for yourself if you get any substantial difference in the first place.

[blake.mcmurray]

Thank you for the comment.

To be more specific, I am trying to recruit 16s reads from a cyanobacterial metagenomic raw reads so I can do further analysis with that subset of reads. Is that specific enough?