Michael

Hi @AliciaSchep. I have attached the insert length histogram from Picard as well as the model for the NucleoATAC using the default setting under "nucleoatac run'' and when I use...

The RF reads, could they be due to smaller read lengths

Hi Alicia. Thanks, I have been using trim_galore to do the adapter trimming. Would you recommend using the "-nextera" option or the "-a (sequence adapter)." Unless you have another trimming...

Hi @timbitz thanks so much for the swift reply. It took me a little while to test it out as it took a lot longer to run on the servers....

Hi Nicolas, No, using 2.11.4 but using Python 3.7.6. I can see if IT can put an updated version on the server if you think its a HiC-Pro version error?...

Hi Nicolas, Ok tried that and with python 3.7.6: vc7-shared 515 % HiC-Pro-master/HiC-Pro-master_3.0.0/bin/utils/make_viewpoints.py -i pro_merged/hic_results/data/sample1/sample1.allValidPairs -f pro_maps/hic_results/matrix/sample1/raw/20000/sample1_20000_abs.bed -t CapC_Promoter_Oligos_ReF.bed -c -e 1000 -d -v > CapC_Promoters_Oligos.bedgraph Traceback (most recent call...

Hi Nicolas, So have gotten things going, but am getting this error when I use the -e option. I removed the hashes to make it easier to read. vc7-shared 512...

With the updated files, this is what I am now getting. The output files are still empty, except for the file headers. singularity exec /stornext/System/data/apps/HiC-Pro/HiC-Pro-3.0.0/HiC-Pro.sif make_viewpoints.py -i pro_merged/hic_results/data/sample1/sample1.allValidPairs -f pro_maps/hic_results/matrix/sample1/raw/20000/sample1_20000_abs.bed...

Hi Nicolas, Yep, not luck figuring this out. I went through the code and couldn't find anything obvious as to why it wont write the file.

Hi Nicolas, Yes, it does appear to find interaction, but the output files are completely empty. I could send one file over to checkout, do you have an easy transfer...