CheckSingleOrPairEndSeq.r

require(RNAseqData.HNRNPC.bam.chr14)
require(pasillaBamSubset)
require(Rsamtools)

bamFile <- untreated1_chr4()
# نلاحظ أن المجموعة اس هي المتواجدة هنا مما يدل على ان السلاسل احادية النهاية
quickBamFlagSummary(bamFile, main.groups.only = TRUE)
#                                group |    nb of |    nb of | mean / max
#                                   of |  records |   unique | records per
#                              records | in group |   QNAMEs | unique QNAME
#All records........................ A |   204355 |   190770 | 1.07 / 10
#  o template has single segment.... S |   204355 |   190770 | 1.07 / 10   <---
#  o template has multiple segments. M |        0 |        0 |   NA / NA
#      - first segment.............. F |        0 |        0 |   NA / NA
#      - last segment............... L |        0 |        0 |   NA / NA
#      - 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.

# نلاحظ هنا أن السلاسل ثنائية النهاية
bamfile2 <- RNAseqData.HNRNPC.bam.chr14_BAMFILES[1]
quickBamFlagSummary(bamfile2, main.groups.only = TRUE)
#                                group |    nb of |    nb of | mean / max
#                                   of |  records |   unique | records per
#                              records | in group |   QNAMEs | unique QNAME
#All records........................ A |   800484 |   393300 | 2.04 / 10
#  o template has single segment.... S |        0 |        0 |   NA / NA
#  o template has multiple segments. M |   800484 |   393300 | 2.04 / 10  <--
#      - first segment.............. F |   400242 |   393300 | 1.02 / 5
#      - last segment............... L |   400242 |   393300 | 1.02 / 5
#      - 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.