Normalize bigwig track based on coverage

[arpanda]

Hi,
I have few bigwig files with different coverage or read counts and I would like to plot it together. So is there a way to normalize the plots based on coverage or read count?

Thanks
Arijit

[lldelisle]

Hi,
I am not sure I understand what you want but you can use operation. For example, if you have 2 files with 2 and 3 million mapped reads respectively, you can do:

[bigwig1]
file = first.bw
operation = file / 2
min_value = 0
max_value = 10
[bigwig2]
file = second.bw
operation = file / 3
min_value = 0
max_value = 10

[arpanda]

Thanks. I was looking that information only.
In case of missing max_value parameter in merged tracks, max value automatically set from either first or last file. Multiple tracks are merged using overlay_previous = share-y

Is it possible to automatically set the max value from the multiple tracks instead of specifying it? as In some cases, we do not know the max value. setting one such value, can be too small or high.

[lldelisle]

For the moment, no...
#321 also request group scaling which is roughly the same. You can find a temporary solution there.
I close the issue but you can reopen it.