Rsamtools
を使った判定法
> packageVersion("Rsamtools") [1] ‘1.20.5’
library(Rsamtools) # ファイルのPATHを指定 fl <- system.file("extdata", "ex1.bam", package="Rsamtools") > quickBamFlagSummary(fl) group | nb of | nb of | mean / max of | records | unique | records per records | in group | QNAMEs | unique QNAME All records........................ A | 3307 | 1699 | 1.95 / 2 o template has single segment.... S | 0 | 0 | NA / NA o template has multiple segments. M | 3307 | 1699 | 1.95 / 2 - first segment.............. F | 1654 | 1654 | 1 / 1 - last segment............... L | 1653 | 1653 | 1 / 1 - other segment.............. O | 0 | 0 | NA / NA Note that (S, M) is a partitioning of A, and (F, L, O) is a partitioning of M. Indentation reflects this. Details for group M: o record is mapped.............. M1 | 3271 | 1699 | 1.93 / 2 - primary alignment......... M2 | 3271 | 1699 | 1.93 / 2 - secondary alignment....... M3 | 0 | 0 | NA / NA o record is unmapped............ M4 | 36 | 36 | 1 / 1 Details for group F: o record is mapped.............. F1 | 1641 | 1641 | 1 / 1 - primary alignment......... F2 | 1641 | 1641 | 1 / 1 - secondary alignment....... F3 | 0 | 0 | NA / NA o record is unmapped............ F4 | 13 | 13 | 1 / 1 Details for group L: o record is mapped.............. L1 | 1630 | 1630 | 1 / 1 - primary alignment......... L2 | 1630 | 1630 | 1 / 1 - secondary alignment....... L3 | 0 | 0 | NA / NA o record is unmapped............ L4 | 23 | 23 | 1 / 1
single segmentだけ:シングルエンド multiple segmentだけ:ペアエンド
とりあえず知りたい
testPairedEndBam(fl) [1] TRUE