![]() ![]() The options include our original normalization scheme ( Lieberman-Aiden and Van Berkum et al., 2009), as well as a matrix balancing scheme that ensures that each row and column of the contact matrix sums to the same value ( Knight and Ruiz, 2012). Juicer can adjust for these biases in multiple ways. Due to factors such as chromatin accessibility, certain loci are observed more frequently in Hi-C experiments. These loci correspond to the rows and columns of a contact matrix each entry in the matrix reflects the number of contacts observed between the corresponding pair of loci during a Hi-C experiment. To do so, the linear genome is partitioned into loci of a fixed size, or “resolution,” (e.g., 1Mb or 1Kb). Next, the catalog of contacts is used to create contact matrices. When appropriate hardware is available, this procedure can be accelerated, either by parallelizing across multiple CPUs or by using an FPGA (see Table 1). To accomplish this, read pairs are aligned to the genome both duplicates and near-duplicates are removed, and read pairs that align to three or more locations are set aside. Juicer comprises three tools, which are designed to be run one-after-another.įirst, Juicer transforms raw sequence data into a list of Hi-C contacts (pairs of genomic positions that were adjacent to each other in three-dimensional space during the experiment). Juicer is also compatible with a variety of cloud and cluster architectures. In order to meet the engineering challenge of handling such massive datasets, Juicer supports the use of parallelization and hardware acceleration whenever possible, including CPU clusters, general-purpose graphics processing units (GP-GPUs), and field-programmable gate arrays (FPGAs). Juicer is closely based on the algorithms that we recently developed in order to analyze and annotate our terabase-scale Hi-C experiments ( Rao and Huntley et al., 2014). Here, we introduce Juicer, an easy-to-use, fully-automated pipeline for the processing and annotation of data from Hi-C and other contact mapping experiments. Ensuring such compatibility can be a considerable engineering challenge. #File juicer 4 software#Moreover, when designing tools that require high-performance computation, ensuring reliability and ease-of-use across software platforms and hardware instances becomes a crucial desideratum. In contrast, we recently generated 6.5 billion reads and 1.6 Tb of DNA sequence in order to create a single 3D map of the genome at kilobase resolution ( Rao and Huntley et al., 2014).Īlthough pipelines for Hi-C data analysis exist ( Lieberman-Aiden and Van Berkum et al., 2009 Schmid et al., 2015 Servant et al., 2015 Suria et al., 2015), these packages are not designed to process datasets at the terabase scale or to annotate the structural features that these maps reflect. Our original maps, derived from 30 million reads and 16 Gb of DNA sequence, described the genome at 1 megabase resolution ( Lieberman-Aiden and Van Berkum et al., 2009). ![]() The resulting maps reflect patterns of physical contact between loci, making it possible to deduce how loci are organized in 3D.Įfforts to improve the resolution of 3D maps have caused the amount of DNA sequence produced from Hi-C experiments to skyrocket. Or if this is just faster than copying and pasting from the file.Hi-C experiments probe the three-dimensional structure of DNA and chromatin by ligating and sequencing DNA loci that are spatially proximate to one another ( Lieberman-Aiden and Van Berkum et al., 2009 Rao and Huntley et al., 2014). ![]() #File juicer 4 windows#If you receive "self extracting" EXE files designed for Windows If you have damaged or accidentally erased flash cards for your digital camera If you receive emails with attachments you can not open If you have old files you can no longer open with current applications #File juicer 4 pdf#If you want to extract the images/sounds/videos from a PDF or Word document ![]() File Juicer does't convert the images/sounds/videos it finds, but saves them unchanged in their original format if possible. It finds and extracts: JPEG, JP2, PNG, GIF, PDF, BMP, WMF, EMF, PICT, TIFF, Flash, ZIP, HTML, WAV, AVI, MOV, MP4, MPG, MP3, AIFF, AU, WMV, or text from files which contain data in those formats. In computer forensics this is called carving. Its specialty is to find and extract images, video, audio, or text from files which are hard to open in other ways. File Juicer is a drag-and-drop can opener and data archaeologist. ![]()
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