Signification of Bowtie2 Metrics file

Question

[jlncrnt]

Hello everyone,

I have trouble finding the signification of the fields in the metrics file outputted by bowtie2 (specified with --met-file option).

Below is a plot of all non-zero value of the table rendered by Bowtie2. Whats does DP8ExCell field mean ? Where can I find more infos about fields of the metric file ? I couldn't find any...

Thank you very much

[Devon Ryan]

These are completely undocumented, you'll need to ask the authors.

Answer 1

[cera.fisher]

From the manual: "Having alignment metric can be useful for debugging certain problems, especially performance issues. See also: --met. Default: metrics disabled."

I don't think that the metrics file has much to do with the output of your bowtie2 run, so much as it has to do with tracking the things that bowtie2 did the most in case you need to adjust your parameters or add more threads to make the software run well.

From reading the code, the value in this field represents "// 85. 16-bit SSE seed-extend DP backtrace cells" -- it sounds like it's counting iterations of some step of the algorithm that it uses to extend from a seed sequence. But honestly, that's so deep in the algorithmic math I can't really understand it. The upshot for you as a biologist is that this probably doesn't matter for your data. I'd been recording metrics files and I think I'm going to stop, because from looking at the code it doesn't look like it's counting anything that I really need to know, and since I'm not having any performance issues, why worry?