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This article is about how to analyze ENCODE project. The editor thinks it is very practical, so I share it with you. I hope you can get something after reading this article. Let's take a look at it with the editor.

ENCODE, the abbreviation of Encyclopedia of DNA Elements, is an international cooperative project sponsored by the American Human Genome Research Center (NHGRI). It aims to establish a comprehensive database for human genome data research by integrating DNA, RNA, protein, epigenetic modification and other levels of data.

As shown in the following figure, different groups of data are integrated.

With the continuous development, the data of modENCODE and other projects were integrated one after another, and the database was further expanded to increase the data of mice, fruit flies, nematodes and so on. All data for the project can be queried through the following link

Https://www.encodeproject.org/

Click the Data- > Matrix button to see the results shown below. The filter box on the left can be filtered according to a variety of criteria.

When the filtering is complete, click the number in the right matrix to view the filtered dataset. Taking the chip_seq data of transcription factor CTCF as an example, the results are as follows

For each dataset, the following results are provided

1. Basic information

The basic information such as the data type, the corresponding cell line and tissue type of the sample, and the sequencing platform are given as follows.

two。 Analyzed pipeline

A description of the analysis process used for the dataset is provided, as shown below

3. Related documents

Contains the original sequence of the sequence and the result file of the analysis, which can be downloaded as follows

ENCODE is not only a public database, in addition to providing data retrieval and query services, but also provides different groups of data analysis standards pipeline and various quality control standards for reference.

Using ENCODE, we can carry out data mining based on public database, and we can also refer to its pipeline for data analysis.

The above is how to analyze ENCODE project, the editor believes that there are some knowledge points that we may see or use in our daily work. I hope you can learn more from this article. For more details, please follow the industry information channel.

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