Here we can see a screenshot of Juicebox with the Rao 2017 data loaded and our annotations visualized on the heatmap. The DIRs will appear as blue rectangles on the heatmap. Select chromosome 16 in both drop-down menus below the “Chromosomes” selection toolbar and click the refresh button. After loading it, the “rao2017Annotations.txt” annotations will be shown in the “Select 2D annotation file(s) to open” panel - select it and click the Open button to load in into Juicebox. tab/button, and navigate to the “rao2017Annotations.txt” file. Alternatively, use the View > Show Annotations Panel menu. This file has been pre-generated, right-click and save it from here.Īssuming the “Rao et al. | Cell 2017” “Auxin treated (6 hrs)” data is loaded, click the Show Annotation Panel button at the lower right corner of Juicebox window. This function will create a text file in your working directory containing the annotations which can then be imported into Juicebox. exportJuicebox(rao2017, logfc_cutoff = 2, logcpm_cutoff = 1, p.adj_cutoff = 0.001, file_name = "rao2017Annotations.txt") Say your Hicexp object is named rao2017 simply run the following line of code in R. You will want to select the main map for “Auxin treated (6 hrs)”.Īssuming you have already analyzed the data using multiHiCcompare and you now have a Hicexp object containing the comparison results you can use the exportJuicebox function to export the list of DIRs as an annotations file for input into Juicebox. The Rao 2017 data are available in Juicebox by default under File > Open menu, “Rao et al. | Cell 2017”. We compared the data between the normal HCT-116 cells and the cells treated with auxin for 6 hours. When loaded into Juicebox, users will be able to see the map at fragment resolution.For our example, we will use the data from Rao 2017. The restriction site file data/hg19_MboI.txt should list all of the restriction sites on the hg19 genome, where each line should start with the chromosome name followed by the position of each restriction site on that chromosome, in numeric order, and ending with the size of the chromosome. Reads with one or more end with MAPQ < 30 will not be included. This will produce a file in data/test.hic that can be loaded into Juicebox. Juicebox pre -q 30 -f data/hg19_MboI.txt data/ data/test.hic hg19 Reads with one or more end with MAPQ < 10 will not be included. Juicebox pre -q 10 data/ data/test.hic hg19 It will not include a fragment map and will not filter any of the reads. -c Only calculate map on specific chromosome.-q Filter by MAPQ score greater than or equal to q.-m Only write cells with count above threshold m.Requires restriction site file each line should start with the chromosome name followed by the position of each restriction site on that chromosome, in numeric order, and ending with the size of the chromosome -d Only calculate intra chromosome (diagonal).Alternatively, it should be the chrom.sizes file from UCSC, limited to the chromosomes you'd like to visualize. This is the file you will load into Juicebox. If not using mapping quality filter, mapq will be ignored. If not using the restriction site file option, frag will be ignored. chr = chromosome (must be a chromosome in the genome).str = strand (0 for forward, anything else for reverse).The text file may be gzipped, and should be in the following 11 column format: The optional arguments should go before the required ones. The “pre” command takes three required arguments and a number of optional arguments. (following are adopted from Juicebox website) Once you have the Juicebox command line tool ready, you could use the pre command to generate the HiC file. Java HotSpot(TM) 64-Bit Server VM (build 25.101-b13, mixed mode)įirst you need get Juicebox tool ( ), build the command lines tools following the instructions at Java(TM) SE Runtime Environment (build 1.8.0_101-b13) $ sudo apt-get install oracle-java8-installer $ sudo add-apt-repository ppa:webupd8team/java if you are running Ubuntu, you can follow instructions on this page:. hic URL as custom track, if you see `Error: Error accessing resource` error, most likely your webserver is not allowing CORS access, for Apache server please check and 3 Use Juicebox to prepare the track file.
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