This is not actually an issue, just an optimization or usage question.
I just produced the .pretext file using PretextMap from a BAM (DNase_HiC data) on an assembly (obtained with Salsa2 and with length 2.46Gb). It was pretty straightforward to remap and get the file. Easier than with juicebox. However, the signal in the contact map is a lot lower in PretextView, so it will not help to curate this genome. Although, both maps have 18M contacts in juicebox contact signal stands out a lot more (see the images below)
I have been trying to improve this with the Gamma slide (increasing the medium and maximum values) but this did not help. Is there any way of adjusting the signal and resolution for such cases?
Dear Ed,
This is not actually an issue, just an optimization or usage question.
I just produced the .pretext file using PretextMap from a BAM (DNase_HiC data) on an assembly (obtained with Salsa2 and with length 2.46Gb). It was pretty straightforward to remap and get the file. Easier than with juicebox. However, the signal in the contact map is a lot lower in PretextView, so it will not help to curate this genome. Although, both maps have 18M contacts in juicebox contact signal stands out a lot more (see the images below)
I have been trying to improve this with the Gamma slide (increasing the medium and maximum values) but this did not help. Is there any way of adjusting the signal and resolution for such cases?
PretextView Map
Juicebox Map
Thanks, Fernando