これ、どお?
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Question: What Is The Sequencing 'Depth' ?
I often see the word depth in the manuals of the tools for NGS, what is its meaning ?
thanks.
Eric gives the correct answer for depth (of coverage). I think confusion in this area stems not from the term "depth" but from the term "coverage". Coverage now appears to have 3 meanings:
1.the theoretical "fold-coverage" of a shotgun sequencing experiment: number of reads * read length / target size
2.the theoretical or empirical "breadth-of-coverage" of an assembly: assembly size / target size
3.the empirical average "depth-of-coverage" of an assembly: number of reads * read length / assembly size
(1) and (3) are not the same because of sequencing error & unclonable/unmappable regions of the genome. Lander-Waterman theory deals with the relationship between (1) and (2).
bamCoverageね。
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This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output. The coverage is calculated as the number of reads per bin, where bins are short consecutive counting windows of a defined size. It is possible to extended the length of the reads to better reflect the actual fragment length. bamCoverage offers normalization by scaling factor, Reads Per Kilobase per Million mapped reads (RPKM), counts per million (CPM), bins per million mapped reads (BPM) and 1x depth (reads per genome coverage, RPGC).
このツールは、リーズやフラグメントを入力（BAMファイル）として整列させ、
カバレッジトラック（bigWigまたはbedGraph）を出力として生成します。
カバレッジはリーズ数/ビンとして計算される。ビンは定義された大きさの短い
連続した数えられる小窓である。実際の断片の長さをよりよく反映するように、
リーズの長さを延長することは可能です。 bamCoverageは、scaling factor,
Reads Per Kilobase per Million mapped reads (RPKM), counts per million (CPM),
bins per million mapped reads (BPM) and 1x depth (reads per genome coverage, RPGC).
によって正規化することができます。
はい。ビンの定義だわ。
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bin
synonyms: window, region
A ‘bin’ is a subset of a larger grouping. Many calculations calculation are performed by first dividing the genome into small regions (bins), on which the calculations are actually performed.
遠藤論文に入手経路が書かれている。
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Raw sequencing data from the original RNA-seq experiments examined in this study were downloaded from the short read archive (SRA) at NCBI. The accession number of the project is SRP038104. Genome sequences of mouse (version 38, mm10) obtained from B6 mouse strain were downloaded from NCBI GenBank and encoded into a bowtie database using the bowtie-build (for colored space fastq files) or bowtie2-build (for fastq files) program. The accession numbers (i.e., SRA ID) of the RNA-seq experiments are listed in Table S1 (Supporting Information), and the checksums of archived sequences were confirmed by Dr Teruhiko Wakayama, Yamanashi University, one of the corresponding authors of the original paper.
