bamPEFragmentSize could output the raw fragment metrics

[dpryan79]

Or perhaps just what goes into the histogram, if we precompute that (I need to check). This was requested on the mailing list.

[steffenheyne]

is the number of histogram bins (not the genomic ones) fixed or is this like an auto-estimate? should we allow so influence on the histogram bins? could be useful for the text output....also think of multiqc!?

[dpryan79]

There are already --distanceBetweenBins and --binSize options. Yeah, I'll need to give it a usable header if multiQC is going to be able to grok it.

[steffenheyne]

yes, this is to influence the sampling from the genome, what I meant is if there is any influence on the histogram bins (insert-size bins) in the profile for the output!

[dpryan79]

No, the bins are whatever they end up being.

[dpryan79]

I mean, you can plot the log and set a maximum, but that's it.

[dpryan79]

I'm adding --table and --outRawFragmentLengths options. The first will the metrics in tabular format to a file (rather than the more unstructured format to stdout). The second write a tsv (with a header line to make detection by multiQC easier) with columns, "fragment/read length", "occurrences", "label". That can be easily loaded into R (skip=1).

[dpryan79]

This is now implemented (also in Galaxy) and documented in the develop branch.

[steffenheyne]

great! Could we have easily more stats in the text output like mean and median fragment size? This would make picard a little bit less needed in our workflows...

We should check in detail which metrics from picard CollectInsertSizeMetrics we can easily reproduce...what do you think?

[dpryan79]

Sure, though I expect most of what Picard outputs that's useful is already being output.

…

Sent from my iPhone

On 9. Aug 2017, at 02:03, Steffen Heyne ***@***.***> wrote: great! Could we have easily more stats in the text output like mean and median fragment size? This would make picard a little bit less needed in our workflows... We should check in detail which metrics from picard CollectInsertSizeMetrics we can easily reproduce...what do you think? — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub, or mute the thread.