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2018.05.28 11:54 BED 파일은 어떻게 만드나요? 공유
2018.05.28 11:54 BED 파일은 어떻게 만드나요?

BED 는 유전체 상에서 특정 target region에 대한 위치정보를 나타낸 파일입니다.

BEDTools, SAMTools, BEDOPS 등의 도구를 이용하여 BAM, VCF 파일에서 BED 파일을 만드는 방법도 있지만, raw data가 나오기 전 시퀀싱을 할 때 사용하는 BED 파일을 시퀀싱 업체에서 받아 분석에 적용할 수 있습니다.

만약 BED 포맷을 직접 만드실 때는 아래 필수 컬럼을 확인하시어 만드시면 됩니다.

  1. chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
  2. chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
  3. chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.

    아래는 선택 컬럼입니다.
  4. name - Defines the name of the BED line. This label is displayed to the left of the BED line in the Genome Browser window when the track is open to full display mode or directly to the left of the item in pack mode.
  5. score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray). This table shows the Genome Browser's translation of BED score values into shades of gray:
    shade         
    score in range  ≤ 166167-277278-388389-499500-611612-722723-833834-944≥ 945
  6. strand - Defines the strand. Either "." (=no strand) or "+" or "-".
  7. thickStart - The starting position at which the feature is drawn thickly (for example, the start codon in gene displays). When there is no thick part, thickStart and thickEnd are usually set to the chromStart position.
  8. thickEnd - The ending position at which the feature is drawn thickly (for example the stop codon in gene displays).
  9. itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to "On", this RBG value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome Browser and your Internet browser.
  10. blockCount - The number of blocks (exons) in the BED line.
  11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
  12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
  13. In BED files with block definitions, the first blockStart value must be 0, so that the first block begins at chromStart. Similarly, the final blockStart position plus the final blockSize value must equal chromEnd. Blocks may not overlap.


아래는 excel에서 만든 예시입니다.
예시1)


  예시2)



예시를 참고하여 작성, 저장 후 뒤의 확장자를 BED로 바꿔주시면 됩니다.



추가적으로, BED 포맷에 대한 자세한 설명은 아래를 참고해주십시오.

http://genome.ucsc.edu/FAQ/FAQformat.html#format1

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