bam文件 查看染色体_如何计算bam文件中每个染色体的读取次数？

bam文件 查看染色体

How to count the number of reads in each chromosome in a bam file? The bam file is already sorted by the chromosome names.

如何计算bam文件中每个染色体的读取次数？ bam文件已按染色体名称排序。

If the bam file is indexed, you may quickly get these info from the index:

如果bam文件已建立索引，则可以从索引中快速获取以下信息：

samtools idxstats in.bam | awk '{print $1" "$3}'

If the bam file is not indexed, you may “count” it by uniq:

如果bam文件未建立索引，则可以通过uniq “计数”它：

samtools view in.bam | awk '{print $3}' | uniq -c

(if it is a sam file like in.sam, replace the samtools view in.bam with cat in.sam)

（如果它是in.sam之类的sam文件， samtools view in.bam cat in.sam替换为samtools view in.bam cat in.sam ）

In both cases, samtools provides the tools to parse/show the bam file content.

在这两种情况下， samtools提供了用于解析/显示bam文件内容的工具 。

Answered by Eric Z Ma.

埃里克·马（Eric Z Ma）回答。

翻译自: https://www.systutorials.com/how-to-count-the-number-of-reads-in-each-chromosome-in-a-bam-file/

bam文件 查看染色体