I have this read in my BAM file. It maps on chromosome 1.I open this BAM file in IGV, and I can see the alignment on chromosome 1.But when I open this file in R with Rsamtools:bamContigsCel <- Rsamtools::scanBam('output/alignment/pacbio/bwa/ref     /bristolAssemblySorted.bam', param = Rsamtools::ScanBamParam(what = Rsamtools::scanBamWhat(), flag = Rsamtools::scanBamFlag(isMinusStrand = FALSE), tag = bamTags))[[1]]I then check if the read maps to chromosome 1 in my R object but I cannot find it.bamContigsCel$rname[bamContigsCel$qname == '000000F|arrow'][1] II II IVLevels: I II III IV MtDNA V XBut if I look at the BAM file, it's there. Why isn't Rsamtools importing my read into R?$ samtools view bristolAssemblySorted.bam | grep -n '000000F' | head  -c80000000F|arrow   2064    I   336331  7   2926310H260M1774267H    *   0 0   GAAGCTGTCTAAACTTTGGCCross-posted on biostars
scanBam from Rsamtools is not importing one of my reads into R
r;bam;samtools
Note the flag; that read is mapped in a reverse-complemented manner, so isMinusStrand = FALSE is filtering it out. I tested this by making a BAM file with only that read:@SQ SN:I    LN:1000000000000F|arrow   2064    I   336331  7   2926310H260M1774267H    *   00  *   *Then in R:> library(Rsamtools)> blah = scanBam(foo.bam, param=ScanBamParam(what=scanBamWhat(), flag=scanBamFlag(isMinusStrand = TRUE)))[[1]]> blah$qname[1] 000000F|arrow> blah = scanBam(foo.bam, param=ScanBamParam(what=scanBamWhat(), flag=scanBamFlag(isMinusStrand = FALSE)))[[1]]> blah$qnamecharacter(0)