Costume Center Position of the Interacting Nucleosome

[MogicianEik]

Dear msauria,

At the beginning, I must thank you for all your previous supports that helped me on my analysis and exploration. Currently I must build my own nucleosome-resolved contact matrix from the Hi-C data obtained from the experiment. Due to the experimental assumption, we assumed that the plus and minus strand reads originate from interactions at DNA exit and entry points in nucleosomes are wrapped around the nucleosome. Under this assumption, the center position of the interacting nucleosome can be obtained as 67 bp upstream of the read end coordinates. The assignment was done by finding the closest nucleosome locus along the genome coordinate against the obtained center nucleosome position from each read. I am not sure if your program can add/modify such detailed parameters and create a contact matrix. If not, could you please give me some advice and instructions on creating Hi-C matrix and visualization?

Best regards Eik

[msauria]

If i understand your question correctly, you want to use a custom set of bins based on pre-defined nucleosome positions? If that is the case, then yes, it is possible to due that. You would need a bed file defining nucleosome start and stop positions (I suppose center +/- 67bp). If you wanted all reads assigned to the nearest nucleosome, regardless of distance, you could pass a bed file with just the nucleosome centers and the boundaries would be inferred as the midpoints between adjacent nucleosomes. Alternatively, if you wanted only reads that were close to defined nucleosomes, you could use the nucleosome boundaries and use the "--binned" flag when making the fend file, which allows gaps between adjacent bins.

[MogicianEik]

Thank you for your reply! I will try your way and please allow me to ask you for further questions

Best regards Yichi

On Mon, Mar 11, 2019 at 7:31 AM Michael Sauria notifications@github.com wrote:

If i understand your question correctly, you want to use a custom set of bins based on pre-defined nucleosome positions? If that is the case, then yes, it is possible to due that. You would need a bed file defining nucleosome start and stop positions (I suppose center +/- 67bp). If you wanted all reads assigned to the nearest nucleosome, regardless of distance, you could pass a bed file with just the nucleosome centers and the boundaries would be inferred as the midpoints between adjacent nucleosomes. Alternatively, if you wanted only reads that were close to defined nucleosomes, you could use the nucleosome boundaries and use the "--binned" flag when making the fend file, which allows gaps between adjacent bins.

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[MogicianEik]

Dear Michael,

Thanks for previous hint. Allow me to share my recent progress. I use two bed files defining nucleosome start and stop positions, and I use bedtools closetBed option to find the closest nucleosome per each read pair. Currently I have a result bed file and a restriction_fend file made from the reference genome. Can I visualize my data via your hiFive package?

Best Yichi

[msauria]

If you import the data, yes, you can certainly visualize it with HiFive. Given that you've already mapped your reads to nucleosomes, I would suggest using the RAW data format, which is just chr bin1 bin2 count for each bin-pair containing at least one read. After making a data and project file, you then have the option of using the subcommands hic-interval or hic-heatmap to visualize. Alternatively you could write your own script taking advantage of the HiC.cis_heatmap class function and HiFive.plotting.plot_full_array command (or plot_upper_array, if you get upper-triangle-formatted data back from the cis_heatmap function).