Bedtools-Multicov---reads计数

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bedtools multicov 可以用来对sorted and indexed bam文件依据已有的bed files进行reads计数

bedtools multicov depends upon index BAM files in order to count the number of overlaps in each BAM file. As such, each BAM file should be with either samtools or bamtools.

Usage and option summary

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By default, multicov will report the count of alignments in each input BAM file that overlap.

$ cat ivls-of-interest.bed
chr1 0   10000   ivl1
chr1 10000   20000   ivl2
chr1 20000   30000   ivl3
chr1 30000   40000   ivl4

$ bedtools multicov -bams aln1.bam aln2.bam aln3.bam -bed ivls-of-interest.bed
chr1 0       10000   ivl1         100           2234          0
chr1 10000   20000   ivl2     123           3245      1000
chr1 20000   30000   ivl3      213           2332      2034
chr1 30000   40000   ivl4      335           7654       0

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bedtools multicov will work with a single BAM as well.(单个bam files也是可以的)

$ bedtools   multicov   -bams    aln1.bam   -bed   ivls_of_interest.bed
chr1 0       10000   ivl1    100
chr1 10000   20000   ivl2    123
chr1 20000   30000   ivl3    213
chr1 30000   40000   ivl4    335

来源：[https://bedtools.readthedocs.io/en/latest/content/tools/groupby.html]
参考：http://www.bio-info-trainee.com/745.html