bamPEFragmentSize max fragment size shown on plot

[samuelCollombet]

Would be nice to have the option to change the max value on the x axis.
I am using it to visualized the fragment distribution of ATACseq data, and 2 x mean of fragment size is not enough. I personally change the parameter in the .py file ([mean] x 2 changed for [max]), but it would be ncie to be able to change the parameter on the fly.

[dpryan79]

Indeed, this probably works poorly for ATACseq. Should be an easy enough change. Were you thinking of having some sort of max length parameter or instead one to just change the 2 to some user-specified value? Either would be possible and we can do whichever is preferred.

[samuelCollombet]

In my case I prefer to use the max, so I know what value it is, but it might depends on the user preference.
Also Just realized, havign the possibiltiy ot have the frequency in log scale would be nice :)

[dpryan79]

OK, user-specified max value and a log scale option. Those are quick and easy.

[samuelCollombet]

Cool! Thanks a lot!

[dpryan79]

I just added this to develop both via the CLI and Galaxy. There's now a --maxFragmentLength parameter to set the X axis maximum and a --logScale option that toggles plotting log frequencies. This are both great ideas, thanks for the suggestion!