Hi,
I have been using your excellent NucleoATAC tool, but I wanted to check I have been using the output correctly. I need to assess nucleosome occupancy between different samples.
I have run your software and used the resulting *.occ.bedgraph.gz files, extracting the occupancy scores for the 2bp fragments present in my pre-selected regions of interest. I then aggregated and averaged these scores across all my regions of interest and was able to create a plot showing peaks at the -1 +1 position around selected TSS. So everything seemed correct, but I just wanted to check I was using the correct output files and I had not made an obvious mistake in interpreting the data?
Also, while most of the fragments were 2bp in the *.occ.bedgraph.gz file, a small number were much longer than this. I discarded those long fragments. Was that the correct thing to do?
Many thanks for developing this tool for the community.
Regards,
Steven
Hi,
I have been using your excellent NucleoATAC tool, but I wanted to check I have been using the output correctly. I need to assess nucleosome occupancy between different samples.
I have run your software and used the resulting *.occ.bedgraph.gz files, extracting the occupancy scores for the 2bp fragments present in my pre-selected regions of interest. I then aggregated and averaged these scores across all my regions of interest and was able to create a plot showing peaks at the -1 +1 position around selected TSS. So everything seemed correct, but I just wanted to check I was using the correct output files and I had not made an obvious mistake in interpreting the data?
Also, while most of the fragments were 2bp in the *.occ.bedgraph.gz file, a small number were much longer than this. I discarded those long fragments. Was that the correct thing to do?
Many thanks for developing this tool for the community.
Regards,
Steven