a question about "seven classes of chromatin state"
Hi everyone!
My group received a task about atac-seq and my task is to process data.
now,I am processing data from "Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNDNA-binding proteins and nucleosome position".
I have finished mapping and peak calling, now, I should plot a figure as below.http://greenleaf.stanford.edu/images...thods_fig2.jpg
(a) ATAC-seq fragment sizes generated from GM12878 nuclei. Inset, log-transformed histogram shows clear periodicity persists to six nucleosomes. (b) Normalized read enrichments for seven classes of chromatin state previously defined
The first is ok, but I have no idea about the second. I read the article to find how the seven chromatin state were defined,but failed(what the article said was a little ambiguous,I did not find the exact defination).
BTW,I am a cs student and did not have too much knowledge about biology what should I do to accomplish this figure?
the online methods described below:
ATAC-seq insertion size enrichment analysis within chromatin annotations. First, the distribution of paired-end sequencing fragment sizes overlapping each chromatin state (http://www.ensembl.org/info/docs/fun...mentation.html) were computed. The distributions were then normalized to the percent maximal within each state, and enrichment was computed relative to the genome-wide set of fragment sizes.
THANKS!!
My group received a task about atac-seq and my task is to process data.
now,I am processing data from "Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNDNA-binding proteins and nucleosome position".
I have finished mapping and peak calling, now, I should plot a figure as below.http://greenleaf.stanford.edu/images...thods_fig2.jpg
(a) ATAC-seq fragment sizes generated from GM12878 nuclei. Inset, log-transformed histogram shows clear periodicity persists to six nucleosomes. (b) Normalized read enrichments for seven classes of chromatin state previously defined
The first is ok, but I have no idea about the second. I read the article to find how the seven chromatin state were defined,but failed(what the article said was a little ambiguous,I did not find the exact defination).
BTW,I am a cs student and did not have too much knowledge about biology what should I do to accomplish this figure?
the online methods described below:
ATAC-seq insertion size enrichment analysis within chromatin annotations. First, the distribution of paired-end sequencing fragment sizes overlapping each chromatin state (http://www.ensembl.org/info/docs/fun...mentation.html) were computed. The distributions were then normalized to the percent maximal within each state, and enrichment was computed relative to the genome-wide set of fragment sizes.
THANKS!!
