bamCoverageね。
>>
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。
>>
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。
>>
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.
TSさんの<mergeするとカバレージ倍増。>というのは以下の説明だね。
>>
Merged BAM File
A set of BAM files can now be loaded merged into a single track. If each file contains different Sample or Read Group tags, as specified in the SAM/BAM file format, then the merged track can be sorted by these to differentiate the origins of reads to these files within a single track.
Create a text file containing a list of the BAM files you want to load, listed by either file path or URL. IGV will load all the BAM files as a single track.
This file must be in plain text format with .txt extension. Rich text format will cause an error.
For older versions of IGV, be sure there is not an extra line at the bottom of the list. This causes an error.
If IGV gives an error "Error loading.... Cannot find reader for alignment file" see here.
Required Extension: .bam.list
