Hi there,
First, thanks for such handy tools! We recently changed clusters and with this I upgraded cooler from version 0.8.6 to the most recent version. I'm working with high resolution Micro-C maps, most of which hit more than 10k reads per bin at less than 200 bps resolution, and when scrolling through Higlass I saw some differences between my new and old cool files.
I have checked that this is indeed the mcool file and not Higlass, but there are regions which should be mappable which get covered up (first attached screenshot shows region at 500 bp resolution, top is older version, bottom is newer version). When I zoom in to 125 bp, these regions hidden in the middle of the newer version mcool go away and you can see the signal (screenshot 2). I looked at my logs and saw that these coolers could not converge towards the end (both versions), so I remade cool files starting with 1kb. While these did converge, I had the same issue. I'm not really sure why that is, and was wondering what could have changed between version to cause this? Is it the new use of CLI?
Sometimes these show up where I know there is a region without any mapping, but sometimes these grey lines appear over nicer regions which shouldn't cause any issue, in the region above, to me it looks like it is removing biological signal based on its behavior.
I have also double checked that these don't coincide with blacklisted regions an un-mappable regions.
This is fly data by the way.
Thanks for the help,
Noura
Hi there,
First, thanks for such handy tools! We recently changed clusters and with this I upgraded cooler from version 0.8.6 to the most recent version. I'm working with high resolution Micro-C maps, most of which hit more than 10k reads per bin at less than 200 bps resolution, and when scrolling through Higlass I saw some differences between my new and old cool files.
I have checked that this is indeed the mcool file and not Higlass, but there are regions which should be mappable which get covered up (first attached screenshot shows region at 500 bp resolution, top is older version, bottom is newer version). When I zoom in to 125 bp, these regions hidden in the middle of the newer version mcool go away and you can see the signal (screenshot 2). I looked at my logs and saw that these coolers could not converge towards the end (both versions), so I remade cool files starting with 1kb. While these did converge, I had the same issue. I'm not really sure why that is, and was wondering what could have changed between version to cause this? Is it the new use of CLI?
Sometimes these show up where I know there is a region without any mapping, but sometimes these grey lines appear over nicer regions which shouldn't cause any issue, in the region above, to me it looks like it is removing biological signal based on its behavior.
I have also double checked that these don't coincide with blacklisted regions an un-mappable regions.
This is fly data by the way.
Thanks for the help,
Noura