Mapping issue

[amhaaning]

I have validated that all works as expected with your example data, but it is not working properly with my data. I generated an re database for hg38. I have 300 bp MiSeq reads. Around 95% of all reads start with the reading primer (22 bp) and the first restriction site is 36 bp downstream of the end of the reading primer. I am trimming off the 3' ends of reads (low quality), and all reads are 200 bp after trimming. The fastq import works and looks like the example data. When I tried mapping, reads that contained the 36 bp sequence downstream of the reading primer did not map (~95% of all reads). I tried entering a fake primer sequence in the index.txt file 22 bp upstream of the first restriction site and then cut off all sequence in front of the fake primer. Reads mapped, but 34% were unmapped and none appeared to map to the region surrounding the viewpoint. The nearcis.cover.txt table contains all NaN values. I also tried cutting off all sequence in front of the first restriction site, and zero reads were read in during mapping, despite there clearly being reads in the raw data text file. Do you have any recommendations for getting these reads to map? What would cause zero reads to be read in during mapping or 34% of reads to be unmapped? I analyzed my dataset with pipe4C, and the cis coverage profiles look as expected. We are particularly interested in using your program to create domainograms because they are a lovely visualization. Thanks!