The .nuc file

Then, as you can see, we have now as many nuc files in directory S4/NMalign/ than the number of studied chromosomes. These .nuc files are text files organized as a table which columns are seperated by a single whitespace. From left to right, the meaning of each column is:

1. the reference sequence,
2. the reference chunk index,
3. the ignore status of the reference nucleosome (y=yes/n=no),
4. the outlier status of the reference nucleosome (0=ok,1=outlier),
5. the starting position of the nucleosome on the reference,
6. the ending position of the nucleosome on the reference,
7. the status of the nucleosome on the reference (1=fuzzy, 2=well-localized),
8. the shift in bp between the midpoints of the reference and the corresponding query nucleosomes,
9. the fraction of the insertion/deletion spanning the nucleosome w.r.t the total length of the reference nucleosome,
10. the average probability that the probes covering the reference nucleosome fall into a nucleosome (either fuzzy or well-localized),
11. the query chunk index,
12. the ignore status of the query nucleosome (y=yes/n=no),
13. the outlier status of the query nucleosome (0=ok,1=outlier),
14. the starting position of the query nucleosome on the reference,
15. the ending position of the query nucleosome on the reference,
16. the status of the nucleosome on the query (1=fuzzy, 2=well-localized),
17. the shift in bp between the midpoints of the query and the corresponding reference nucleosomes,
18. the fraction of the insertion/deletion spanning the nucleosome w.r.t the total length of the query nucleosome,
19. the average probability that the probes covering the query nucleosome fall into a nucleosome (either fuzzy or well-localized).
20. if aligned, the p-value of the nucleosome (see next section),
21. if aligned, the effect size corresponding to the p-value (see next section),
22. if aligned, the status of the aligned nucleosome:
    • -1 = insertion/deletion,
    • 0 = fuzzy/fuzzy,
    • 1 = fuzzy/well-localized or well-localized/fuzzy,
    • 2 = well-localized/well-localized,
23. the probability that the region corresponds in fact to a linker / linker configuration,
24. the probability that the region corresponds in fact to a nucleosome (reference) / linker (query) configuration (insertion),
25. the probability that the region corresponds in fact to a linker (query) / nucleosome (reference) configuration (deletion),
26. the probability that the region corresponds in fact to a nucleosome / nucleosome configuration.

Now, we can use the function NMnxcplot of the nucleominer R package to visualize the content of these .nuc files. An exemple is depicted in Figure 8.

Figure: